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Julianna G. Supplee, Pedro Costa-Pinheiro, Karl Wessendorf-Rodriguez, Stephanie Stransky, Qihua Yang, Christina Demetriadou, Nivitha Murali, Joy Li, Jennifer L. Pennise, Mariola M. Marcinkiewicz, Simone Sidoli, Nathaniel W. Snyder, Christian M. Metallo, Ronen Marmorstein, Kathryn E. Wellen. Acetyl-CoA–dependent processes are preferentially supported by local metabolite synthesis. Sci. Adv.12,eaee4935(2026).DOI:10.1126/sciadv.aee4935
Abstract
The cell nucleus is an active metabolic site. Numerous enzymes best known for their roles in cytosolic or mitochondrial pathways also function in the nucleus, where they contribute to gene regulation and DNA replication and repair. Although metabolites can diffuse through nuclear pores, it remains unclear the extent to which the nucleus and cytosol operate as continuous versus distinct metabolic spaces. Both compartments require acetyl-CoA—for example, for histone acetylation and lipid synthesis—and the acetyl-CoA generating enzyme ATP-citrate lyase (ACLY) resides in both locations, but the significance of its dual localization is incompletely understood. Using cell lines in which ACLY is localized to either compartment, we find that ACLY in either location supports fatty acid synthesis and histone acetylation, yet compartment-localized ACLY enables finer control. Nuclear ACLY preserves histone H3K23 acetylation under glucose limitation and modulates specific transcriptional programs, whereas cytosolic ACLY most efficiently supports lipid biosynthetic fluxes. Thus, local synthesis defines a preferential metabolic fate, providing more precise regulation.
Brianna Hill-Payne, Mohd. Younis Bhat, George M. Burslem; General Strategy for Controlling Functional Lysine Acetylation via Induced Proximity. ACS Chem. Biol. 2026; https://doi.org/10.1021/acschembio.6c00510
Abstract
Assigning causal function to post-translational modifications (PTMs) remains a central challenge in molecular biology, as most modification events cannot be readily interrogated in their native cellular context. Here, we present a generalizable chemical biology strategy for investigating the functional consequences of lysine acetylation through programmable induced proximity. By combining modular effector recruitment with chemically controlled proximity, this approach enables systematic elucidation of how enzyme identity shapes acetylation outcomes on target proteins in living cells. Across multiple substrates, including histone H3 and p53, we find that distinct acetyltransferases generate reproducible and target-dependent site-selective acetylation patterns, indicating that effector identity encodes predictable features of modification outcomes. These observations establish a framework for linking enzyme recruitment to site-specific PTM deposition and provide a route to identify candidate functional modification events. Rather than providing a single mechanistic insight, this work introduces a broadly applicable strategy for interrogating causal relationships between proximity-driven enzyme recruitment and protein modification, as demonstrated by the impact of p53 acetylation on downstream transcripts. This platform is readily extensible to additional effectors and targets and enables systematic discovery of functional PTMs in cellular systems.
Qi Qiu, Hongjie Zhang, Zijie Xia, William Gao, Julia I. Leu, Dongming Liang, Ying Li, Fan Li, Yijing Su, Emily Feierman, Erin Van Horn, Guo-li Ming, Erica Korb, Hongjun Song, Zhaolan Zhou, Hao Wu. Spatial mapping of RNA turnover kinetics in the mouse brain. Nat Neurosci (2026). https://doi.org/10.1038/s41593-026-02420-y
Abstract
Gene regulation requires coordinated control of RNA synthesis and degradation, yet measuring RNA turnover across intact tissues remains challenging. Here we present spatial NT-seq, a method that combines transgenesis-free metabolic RNA labeling with in situ chemical recoding on spatial transcriptomics platforms to co-map newly synthesized and pre-existing RNAs. Applying spatial NT-seq to the mouse brain reveals pronounced regional heterogeneity in RNA turnover and identifies the dentate gyrus as a spatial hotspot marked by coordinated upregulation of basal RNA synthesis and decay. Moreover, spatial NT-seq uncovers rapid, brain region-specific transcriptional and post-transcriptional responses to electroconvulsive stimulation, a clinically relevant treatment for refractory depression. Finally, we leverage computational modeling to identify sequence features and post-transcriptional regulators that shape transcriptome-wide mRNA stability across spatial and cellular contexts in the mouse brain. Together, this integrated ‘in vivo timescope’ framework provides a spatially resolved view of RNA turnover kinetics and reveals the regulatory architecture of RNA stability in vivo.
Zhendong Cao, Kurtis N McCannell, Sixiang Yu, Krista A Budinich, Won Jun Kim, Yuqing Jing, Michelle Y Wang, Steven Tittley, Zhuoyu Wen, Kathy Fange Liu, Junwei Shi, Omar Abdel-Wahab. PTBP1 controls oncogenic transcript processing and maintenance of acute myeloid leukemia. Leukemia. 2026 Aug 24. doi: 10.1038/s41375-026-03098-8. Epub ahead of print. PMID: 42637878.
Abstract
RNA-binding proteins are critical regulators of gene expression in both normal physiology and cancer. Here we set out to systematically annotate the functions of RNA-associated proteins across multiple cancer types via domain-focused CRISPR screens targeting RNA-modifying enzymes and RNA-binding proteins. We utilized 3182 sgRNAs targeting 527 RNA-enzymatic and binding domains in 341 RNA-associated proteins and identified multiple RNA-binding proteins as dependencies in acute myeloid leukemia (AML), including the RNA splicing factor PTBP1 and the N6-methyladenosine reader RBM15, with a bias toward the aggressive KMT2A-rearranged (KMT2A-r) subtype of AML. Genetic and cellular validation confirmed all four RNA-binding domains of PTBP1 as required for KMT2A-r AML proliferation. In contrast to the lack of requirement for PTBP1 in myelopoiesis, PTBP1 suppression in AML caused cell cycle arrest, apoptosis, and induction of myeloid differentiation programs. Transcriptomic analysis revealed that PTBP1 loss disrupted the KMT2A-r-essential transcriptional program and caused widespread dysregulation of splicing. CLIP-seq analysis further identified that PTBP1 preferentially binds to a subset of transcripts critical for KMT2A-r AML proliferation, including IKZF1, MEF2C, EZH2, SIK3, and PBX3. Collectively, these findings demonstrate that PTBP1 supports AML proliferation by fine-tuning the expression and splicing of AML-essential genes, providing a workflow for systematically annotating RNA-associated protein dependencies in cancer.
Jenna N Beyer, Kaitlyn Toy, George M Burslem. A Protein Editing Method to Modify Proteins in Live Mammalian Cells. Curr Protoc. 2026 Aug;6(8):e70443. doi: 10.1002/cpz1.70443. PMID: 42627710; PMCID: PMC13496354.
Abstract
Protein editing, as mediated by protein trans‐splicing, offers the ability to manipulate, label, and modify proteins in vitro and in live mammalian cells. This ability to observe and control proteins with this high resolution is a burgeoning area of interest within the chemical biology field. In this protocol, we outline the general approach for setting up a cellular protein editing experiment, emphasizing the planning process for a successful protein editing experiment. Additionally, we include methods to install and subsequently label a click chemistry handle p‐azido‐phenylalanine, a non‐canonical amino acid (ncAA) within the intein donor, such that this ncAA and any label can be edited into a protein in live mammalian cells. Overall, we anticipate that this protocol should serve as a generalizable roadmap for planning and carrying out a protein editing experiment.
Brianna Hill-Payne, Mohd. Younis Bhat, George M. Burslem; General Strategy for Controlling Functional Lysine Acetylation via Induced Proximity. ACS Chem. Biol. 2026; https://doi.org/10.1021/acschembio.6c00510
Abstract
Pengfei Guo, Yan Cui, Jincan He, Abraham J Waldman, Jiaxin Zhu, Yufan Chen, Zhi Huang, Jingtian Zhou, Jennifer E Phillips-Cremins, Yanxiang Deng. Integrative spatial profiling of 3D genome organization and gene expression in tissue. Cell. 2026 Aug 25. doi: 10.1016/j.cell.2026.07.039.
Summary
Three-dimensional genome organization shapes transcriptional regulation, yet measuring its spatial coordination in situ within intact tissues remains challenging. We present Spatial Hi-C-RNA, a multimodal platform that simultaneously maps genome-wide chromatin contacts and transcriptomes from the same tissue section at near-single-cell resolution. Across the mouse brain, developing embryos, and human melanoma, Spatial Hi-C-RNA generated multimodal maps that aligned with tissue anatomy while revealing complementary chromatin- and RNA-defined spatial patterns. Multiscale features, including A/B compartments, topologically associating domains, and chromatin loops, were associated with region- and cell-type-specific transcriptional programs. In mouse embryos, Spatial Hi-C-RNA resolved coordinated chromatin and transcriptional remodeling during neuronal maturation across developmental stages. In human melanoma, chromatin architecture delineated intratumoral subregions not detected by RNA alone and linked tumor-state transitions to changes in compartments, domain boundaries, and regulatory programs. Spatial Hi-C-RNA thus provides a broadly applicable framework for investigating genome structure-function relationships in development and disease within native tissue environments.
Atishay Jay, Yeqiao Zhou, Sora Yoon, Bereketab N Abeje, Aditi Chandra, Michael F Michieletto, Julia Wald, Jorge Henao-Mejia, Arjun Raj, Robert B Faryabi, Golnaz Vahedi. Single-allele chromatin tracing reveals cytokine-dependent super-enhancer repositioning in CD4+ T cells. Immunity. 2026 Aug 24:S1074-7613(26)00323-7. doi: 10.1016/j.immuni.2026.08.001. Epub ahead of print. PMID: 42636801.
Abstract
Naive CD4+ T cells interpret cytokine cues to commit to T helper lineages. Here, we examined the impact of cytokines on the Ets1-Fli1 locus, which encodes paralogous transcription factors essential for T cell effector responses. Epigenomic and chromatin interaction profiling in double-positive (DP) thymocytes defined a T cell super-enhancer and a CTCF-bound boundary. Chromatin tracing at single-allele resolution revealed concurrent multi-way interactions among Ets1, Fli1, and the super-enhancer coupled to transcription. Deleting the CTCF boundary decompacted the locus without altering Ets1 expression or T cell development, whereas deleting the super-enhancer drew Ets1 and Fli1 closer; promoter proximity increased Ets1-Fli1 co-expression. In CD4+ Th1 cells, cytokines increased multi-way interactions and repositioned the super-enhancer toward the geometric center, activating both paralogs. Super-enhancer deletion rendered Th1 cells structurally and transcriptionally DP like. Thus, cytokines can drive lineage-specific gene activation by repositioning a super-enhancer, providing a mechanistic framework for how noncoding variants at the Ets1-Fli1 locus contribute to CD4+ T cell-mediated immune disorders.
Zachary Gardner, Ricardo Linares-Saldana, Krishna Kumar Haridhasapavalan, Pedro O Méndez Fernández, Vasia Barka, Rachel Yang, Bailey Koch-Bojalad, Arun Padmanabhan, Qiaohong Wang, Parisha P Shah, Son C Nguyen, Eric F Joyce, Rajan Jain. Genome folding and nuclear speckles converge to orchestrate fibroblast activation. Sci Adv. 2026 Aug 14;12(33):eaec3453. doi: 10.1126/sciadv.aec3453. Epub 2026 Aug 14. PMID: 42599997; PMCID: PMC13475600.
Abstract
Fibroblasts adopt diverse cell states in response to inductive cues to maintain tissue homeostasis. We leveraged this cell-state plasticity to define how genome organization contributes to changes in cellular identity. We show that TGF-β reconfigures topologically associating domains and chromatin loops at genes upregulated during fibroblast activation into myofibroblasts. Cohesin is required for gene induction during fibroblast activation, and enhanced cohesin stability is sufficient to bypass TGF-β signaling and drive a myofibroblast-like state. Emerging evidence suggests chromatin spatial positioning relative to nuclear speckles can regulate gene expression. Therefore, we examined the role of the critical nuclear speckle component SON and showed that it is required for myofibroblast gene expression. Notably, enhancing genome folding partially rescued gene expression in fibroblasts with SON-depleted nuclear speckles. Together, these findings advance our understanding of fibrosis and support a model in which distinct facets of genome organization converge to orchestrate cell-state transitions.
Jordi C J Hintzen, George M Burslem. Beyond acetylation: Evaluating the emerging biology of lysine acylation. Cell Chem Biol. 2026 Aug 12:S2451-9456(26)00282-5. doi: 10.1016/j.chembiol.2026.07.009. Epub ahead of print. PMID: 42586062.
Abstract
Lysine acylation has emerged as a rapidly expanding family of post-translational modifications that directly links cellular metabolism to protein regulation. Beyond lysine acetylation, advances in mass spectrometry and chemical biology have uncovered a diverse repertoire of acyl modifications spanning short-chain, branched, unsaturated, aromatic, and dicarboxylic groups. Together these modifications establish lysine acylation as a molecular interface through which metabolic state can shape protein function, chromatin regulation, and cell signaling. Yet fundamental questions remain regarding their biological significance, enzymatic regulation, site specificity, and whether many acylations function as bona fide regulatory signals or reflect metabolite-driven mechanisms. Here, we synthesize the current understanding of the metabolic origins, structural and biochemical properties, and their writer, reader, and eraser systems that govern lysine acylations. We further highlight emerging chemical biology approaches for detecting, manipulating, and functionally interrogating acyl marks and discuss the conceptual and technological advances needed to distinguish closely related modifications and establish their causal biological roles.
Diana B Voss, Emily J Shields, Andrey Poleshko, Li Li, Jun Li, Roger Wang, Mariacristina Calcagno, Rajan Jain, Cheryl L Smith, Jonathan A Epstein. Combined loss of histone methyltransferases GLP and G9a disrupts neural crest cell fate determination. J Clin Invest. 2026 Aug 13:e205970. doi: 10.1172/JCI205970. Epub ahead of print. PMID: 42593859.
Mingyang Zhou, Supuni Thalalla Gamage, Khoa A Tran, David Bartee, Xuepeng Wei, Boyu Yin, Shelley Berger, Jordan L Meier, and Ronen Marmorstein. Structure of the NAT10 acetyltransferase and mechanism of tRNA acetylation. Nat Commun. 2026 Jun 20;17(1):7763. doi: 10.1038/s41467-026-74222-6. PMID: 42321159; PMCID: PMC13433802.
Abstract
NAT10 is the sole eukaryotic acetyltransferase that catalyzes N4-acetylcytidine (ac4C) modification of RNA. While dysregulation of NAT10 is associated with cancer and premature aging syndromes, the requirement for its acetyltransferase activity and how NAT10 coordinates catalysis and RNA binding remain poorly understood. Here, we report single particle cryo-electron microscopy structures of eukaryotic (Chaetomium thermophilum) NAT10 in complex with a designer cytidine-CoA cofactor-based ligand in the presence and absence of ADP. NAT10 forms a symmetrical heart-shaped dimer where a Gcn5-related N-acetyltransferase (GNAT) domain with an atypically opened active site is flanked by conserved helicase and RNA-binding domains. Biochemical reconstitution of NAT10 in the presence of the adapter protein THUMPD1 reveals that tRNA acetylation is enabled by two conserved active site residues (His548 and Tyr549 in CtNAT10) and two basic patches: one proximal and one distal from the active site, and suggests that binding orientation rather than affinity drives catalysis. Finally, we harness structure-guided mutations in cellular studies to demonstrate the necessity for NAT10 catalytic acetyltransferase activity in fungal thermoadaptation and mammalian etoposide-induced cellular senescence, respectively. Our findings provide a structural foundation for understanding NAT10-catalyzed cytidine acetylation, with implications for regulation and therapeutic targeting of its distinct RNA acetyltransferase activity.
Gao S, Oshima KK, Chuang SC, Loftus M, Potapova TA, Montanari A, Gordon DS, Yang Z; Human Genome Structural Variation Consortium; Human Pangenome Reference Consortium; Mao Y, Hsieh P, Gerton JL, Konkel MK, Ventura M, Logsdon GA. A global view of human centromere variation and evolution. Nature. 2026 Jul 29. doi: 10.1038/s41586-026-10841-9. Epub ahead of print. PMID: 42527608.
Abstract
Centromeres are essential chromosomal regions that ensure accurate chromosome segregation during cell division, yet their highly repetitive sequence has historically hindered their complete assembly and characterization1. Consequently, the full spectrum of centromere diversity across individuals, populations and evolutionary contexts remains largely unexplored. Here we address this gap in knowledge by assembling and characterizing 2,110 centromeres from diverse individuals representing 5 continental and 28 population groups. Using bioinformatic tools tailored for centromeres, we identify variation, including 226 centromere haplotypes and 1,870 α-satellite higher-order repeat variants. While most centromeres have a single kinetochore site, we find that around 6% have di-kinetochores, and less than 1% have tri-kinetochores, which we confirm using long-read chromatin profiling and multigenerational inheritance. We also show that kinetochore position is closely associated with the underlying sequence and structure of the centromere. To understand the nature of evolutionary change, we compared these centromeres to 5,747 centromeres assembled by the Human Pangenome Reference Consortium. We show that centromeres have a 20-fold variation in mutation rate, and a subset of centromeres has evidence of archaic hominin introgression. We validate these mutation rates in a 4-generation, 28-member family and show that the kinetochore site is the most rapidly mutating region in the centromere. We propose a model that reveals an ‘arms race’ between centromeric sequence and proteins, with frequent mutations within the kinetochore site that lead to changes in genetic and epigenetic landscapes and, ultimately, rapid evolution of these critically important regions.
Prasasya RD, Kim JJ, Liu Z, Kohli RM, Bartolomei MS. TET1 noncatalytic activity shapes the chromatin landscape associated with de novo methylation establishment in the male germline. Genes Dev. 2026 Aug 3;40(15-16):1202-1213. doi: 10.1101/gad.353483.125. PMID: 42448565; PMCID: PMC13374711.
Abstract
In the germline, DNA methylation is globally erased in primordial germ cells (PGCs), enabling establishment of sex-specific methylomes in prospermatogonia or oocytes. The catalytic activity of TET1 is required for complete demethylation in PGCs, yet sperm from Tet1 -/- mice display methylation defects not explained by incomplete erasure. Instead, these defects arise from abnormal de novo methylation during development, coinciding with erosion of H3K4me3, a chromatin modification that blocks DNMT3A/3L. Using a catalytically inactive Tet1 HxD mouse line, we demonstrate a noncatalytic role of TET1 in promoting H3K4me3 deposition and protecting a subset of sperm hypomethylated regions from aberrant methylation in prospermatogonia.
Xuerui Wu, Eric L Waite, Mark Tigue, Benjamin Glaser, Dana Avrahami, Klaus H Kaestner. The SenKiller Mouse: Enabling Cell Type-Specific Ablation of Senescent Cells. Cell Mol Gastroenterol Hepatol. 2026 Aug 5:101855. doi: 10.1016/j.jcmgh.2026.101855. Epub ahead of print. PMID: 42556640.
Natalie E Toothacre, Kiara L Rodríguez-Acevedo, Keenan J Wiggins, Christopher D Scharer, Montserrat C Anguera. Xist RNA dependent and independent mechanisms regulate dynamic X chromosome inactivation in B lymphocytes. Cell Rep. 2026 Apr 9;45(4):117254. doi: 10.1016/j.celrep.2026.117254. Epub ahead of print. PMID: 41964951; PMCID: PMC13142736.
Abstract
X chromosome inactivation (XCI) equalizes X-linked gene expression between the sexes through heterochromatic mark accumulation. XCI is dynamic in female B cells, as cytological enrichment of Xist RNA and heterochromatic marks on the inactive X chromosome (Xi) are absent in naive B cells yet return following stimulation. Here, we asked whether heterochromatic histone marks are present on the Xi in naive B cells and whether Xist RNA is required for their deposition and retention following stimulation. We find that the Xi in naive B cells is depleted for H2AK119Ub and H3K9me3 but enriched for DNA methylation and H3K27me3, which maintain an Xist RNA-dependent memory of XCI. Upon stimulation, Xist-independent H3K27me3 and Xist-dependent H2AK119Ub modifications accumulate across the Xi with temporal and spatial specificity. Our findings reveal the importance of Xist RNA, H3K27me3, and H2AK119Ub marks for Xi gene regulation following female B cell stimulation.
Mingyang Zhou, upuni Thalalla Gamage, Khoa A Tran, David Bartee, Xuepeng Wei, Boyu Yin, Shelley Berger, Jordan L Meier, Ronen Marmorstein. Structure of the NAT10 acetyltransferase and mechanism of tRNA acetylation. Nat Commun. 2026 Jun 20. doi: 10.1038/s41467-026-74222-6. Epub ahead of print. PMID: 42321159.
Abstract
NAT10 is the sole eukaryotic acetyltransferase that catalyzes N4-acetylcytidine (ac4C) modification of RNA. While dysregulation of NAT10 is associated with cancer and premature aging syndromes, the requirement for its acetyltransferase activity and how NAT10 coordinates catalysis and RNA binding remain poorly understood. Here, we report single particle cryo-electron microscopy structures of eukaryotic (Chaetomium thermophilum) NAT10 in complex with a designer cytidine-CoA cofactor-based ligand in the presence and absence of ADP. NAT10 forms a symmetrical heart-shaped dimer where a Gcn5-related N-acetyltransferase (GNAT) domain with an atypically opened active site is flanked by conserved helicase and RNA-binding domains. Biochemical reconstitution of NAT10 in the presence of the adapter protein THUMPD1 reveals that tRNA acetylation is enabled by two conserved active site residues (His548 and Tyr549 in CtNAT10) and two basic patches: one proximal and one distal from the active site, and suggests that binding orientation rather than affinity drives catalysis. Finally, we harness structure-guided mutations in cellular studies to demonstrate the necessity for NAT10 catalytic acetyltransferase activity in fungal thermoadaptation and mammalian etoposide-induced cellular senescence, respectively. Our findings provide a structural foundation for understanding NAT10-catalyzed cytidine acetylation, with implications for regulation and therapeutic targeting of its distinct RNA acetyltransferase activity.
Aoife O’Farrell, Zijian Niu, Arjun Raj. Quantitative cytokine profiling of primary human macrophages reveals distinct single-cell modes of trained immunity. Cell Syst. 2026 Jun 23:101648. doi: 10.1016/j.cels.2026.101648. Epub ahead of print. PMID: 42335896.
Abstract
Macrophages can remember prior activation and subsequently augment their response to restimulation through trained immunity. However, it remains uncertain how trained immunity phenotypes manifest in individual cells. Here, we leverage highly quantitative single-molecule RNA imaging across 90,857 individual macrophages from 26 human donors to reveal inflammatory response dynamics in trained vs. untrained populations at single-cell resolution. Different inflammatory response genes showed distinct single-cell behavior in trained populations upon restimulation. Although training increased transcription of these response genes early after restimulation, untrained populations eventually “caught up” to the transcriptional output of trained populations, highlighting the importance of sampling timescale when interpreting transcriptional assays of training. Training did not significantly alter the relationship between the transcriptional activation of different genes within the same single cell, and any single cell appeared to be capable of training. Overall, these results revealed gene-specific single-cell transcriptional changes that generate population-wide training phenotypes in macrophages.
Ryan H Boe, Catherine G Triandafillou, Rossana Lazcano, Jennifer A Wargo, Arjun Raj. Spatial transcriptomics reveals influence of microenvironment on intrinsic fates in melanoma therapy resistance. Genome Biol. 2026 May 23. doi: 10.1186/s13059-026-04112-z. Epub ahead of print. PMID: 42174697
Abstract
Resistance to cancer therapy is driven by both cell-intrinsic and microenvironmental factors. We use spatial transcriptomics and single-cell RNA sequencing to uncover distinct resistance programs in melanoma cells shaped by intrinsic cellular states and the tumor microenvironment. Consensus non-negative matrix factorization reveals shared intrinsic resistance programs across cell lines. In patient samples, these resistance programs coexist within individual tumors and associate with diverse immune signatures. Single-cell resolution spatial transcriptomics in xenograft models reveals both intrinsically determined and extrinsically influenced resistant fates. This work demonstrates that therapy-resistant fates coexist within distinct microenvironments and that tissue features influence which fate is adopted.
Aoife O’Farrell, Zijian Niu, Jingxin Li, Laura C Van Eyndhoven, Kavitha Sarma, Arjun Raj. Human macrophages encode stimulus-specific information of prior exposures through trained immunity. Cell Syst. 2026 Jun 19:101647. doi: 10.1016/j.cels.2026.101647. Epub ahead of print. PMID: 42320478.
Abstract
Trained immunity (a form of innate immune memory) is defined in part by heightened responses to pathogen restimulation and can be generated by many different stimuli. However, both the quantitative differences in trained states generated by different stimuli and the downstream consequences of those differences remain unclear. Here, we used primary human monocyte-derived macrophages to demonstrate phenotypic and molecular stimulus specificity of trained immunity 6 days after initial exposure. Quantification of cytokine production with single-molecule RNA imaging revealed stimulus-specific patterns of response to restimulation, with trained cells showing stronger responses to secondary stimuli more similar to their initial stimulation. Differential licensing of inflammatory transcription factors was associated with encoding of specificities in chromatin 6 days after training, while memory of some, but not all, training stimuli was lost by 11 days post-training in vitro. Overall, our findings demonstrate that different training stimuli can impart specific memories that generate distinct training phenotypes.
Bing-Rui Zhou, Edgar Luzete-Monteiro, Jingchao Zhang, Naomi Takenaka, Hsin-Yao Tang, Meilin Fernandez Garcia, Mariel Coradin, Megan Frederick, Greg Donahue, Benjamin Garcia, Yawen Bai, Kenneth S. Zaret. Distinct associations of pioneer factor Ascl1-E12a with nucleosomes drive changes in cell fate. Mol Cell. 2026 Jun 12:S1097-2765(26)00344-8. DOI: 10.1016/j.molcel.2026.05.020. Epub ahead of print. PMID: 42285106.
Abstract
Understanding how pioneer transcription factors target nucleosomal DNA and initiate chromatin accessibility reveals the earliest events in cell fate changes. We integrated structural, biochemical, and genomic approaches to assess how the pioneer factor Ascl1-E12a heterodimer perturbs nucleosomes in vitro and in vivo to induce a neural cell fate. Two Ascl1-E12a heterodimers shift and unwrap 15 bp of nucleosomal DNA in a stepwise manner while eliciting solvent exchanges within the octamer. Nucleosome binding, but not free DNA binding, by Ascl1-E12a is enhanced by two types of associations with the nucleosome that differentially affect the kinetics of DNA unwrapping and shifting. Nucleosome association mutants of Ascl1 perturb chromatin opening on linker histone-compacted nucleosome arrays-independent of nucleosome remodelers-and targeting of closed chromatin in vivo, with consequent deficiencies in cellular reprogramming. Our findings establish that distinct associations with nucleosomes are essential for the pioneer factor Ascl1 to overcome chromatin barriers to reprogram cell fate.
Claudia D. Lovell, Nikhil Jiwrajka, Natalie E. Toothacre, Hayley K. Amerman, Michael P. Cancro, Montserrat C. Anguera. Female mice with a Xist deletion in B cells can develop lupus-associated phenotypes. Cell Reports, Volume 45, Issue 6, 2026, 117517, ISSN 2211-1247. DOI: https://doi.org/10.1016/j.celrep.2026.117517. (https://www.sciencedirect.com/science/article/pii/S2211124726005954)
Summary
Systemic lupus erythematosus (SLE) is an autoimmune disease preferentially observed in women. X-linked gene expression in XX females is equalized with that in XY males by X chromosome inactivation (XCI). However, B cells from female patients with SLE and mouse models of SLE exhibit aberrant X-linked gene expression and mislocalization of Xist RNA, a critical regulator of XCI, suggesting that impaired XCI may contribute to the disease. Here, some female mice harboring a B cell-specific Xist deletion (“Xist cKO”) spontaneously developed SLE phenotypes, including expanded activated B cell subsets, disease-specific autoantibodies, and glomerulonephritis. Pristane treatment of Xist cKO mice led to an increased expansion of activated B cell subsets, resulting in higher anti-dsDNA autoantibody production. Activated B cells from Xist cKO mice with SLE phenotypes had an increased expression of X-linked and autosomal genes, depletion of X-linked H3K27me3, and were more responsive to stimulation. This work suggests that impaired XCI maintenance in B cells directly contributes to SLE-associated phenotypes in a female-biased manner.
Krista A. Budinich, Xinyi Yao, Chujie Gong, Lele Song, Xiaoting Wang, Michelle C. Lee, Kaeli M. Mathias, Qinglan Li, Sylvia Tang, Yiman Liu, Son C. Nguyen, Eric F. Joyce, Yuanyuan Li, Haitao Li, Liling Wan.
RNA reinforces condensate nucleation on chromatin to amplify oncogenic transcription, Molecular Cell, 2026, ISSN 1097-2765, DOI: https://doi.org/10.1016/j.molcel.2026.05.024 (https://www.sciencedirect.com/science/article/pii/S1097276526003485)
Summary
Aberrant chromatin-associated condensates have emerged as drivers of transcriptional dysregulation in cancer, yet how extrinsic factors modulate their assembly and function remains poorly understood. Gain-of-function mutations in the chromatin reader ENL (“Eleven-nineteen-leukemia”) drive oncogenesis by inducing condensate formation at select target loci. Here, we demonstrate that locally produced transcripts reinforce the nucleation, chromatin engagement, and oncogenic activity of mutant ENL condensates. Mutant ENL binds to RNA in part through a basic patch within its YEATS domain, and this interaction enhances condensate formation in vitro and in cells. Using a chemically inducible condensate displacement and renucleation system, we show that blocking ENL-RNA interactions or transcription impairs condensate reformation at endogenous targets. RNA binding preferentially enhances mutant ENL occupancy and transcriptional bursting at condensate-permissive loci. In mouse models, disrupting RNA binding suppresses mutant ENL-driven oncogenic transcription and leukemogenesis. These findings reveal how chromatin-associated oncogenic proteins hijack local transcripts to reinforce condensate nucleation and drive tumorigenesis.
Biying Zhu, Na He, Yang Xiao, Bin Chen, Chen Li, Ravi Mandla, Yifan Liu, Jiayu Zhang, Xiao Chang, Fulong Yu, Marijana Vujkovic, Julie A. Lynch, Kyong-Mi Chang, VA Million Veteran Program, Bogdan Pasaniuc, Daniel J. Rader, Mitchell A. Lazar & Wenxiang Hu . Integrative analyses elucidate transcriptional regulatory functions of risk alleles for metabolic liver disease. Nat Genet (2026). https://doi.org/10.1038/s41588-026-02617-8
Abstract
Genome-wide association studies have identified >100 loci associated with metabolic dysfunction-associated steatotic liver disease (MASLD), yet the mechanisms by which noncoding variants alter disease risk remain unclear. Here we map chromatin accessibility in human MASLD liver nuclei, revealing enrichment of risk variants within cell-type-specific regulatory elements bound by lineage-determining transcription factors. Using a massively parallel reporter assay, we identified hundreds of differential activity variants (DAVs) that act in a cell-type-dependent and stimulus-dependent manner and perturb transcriptional regulatory networks linked to liver pathology. Integration of liver expression quantitative trait loci, chromatin looping and single-cell CRISPR interference screening assigns target genes to these DAVs. Importantly, DAVs at numerous loci, including SLC22A3 and key triglyceride metabolism regulators (APOA5, ANGPTL3 and LPL), modulate gene expression, lipid metabolism and hepatic stellate cell activation. Moreover, these DAVs allow improved prediction of MASLD risk. These results define a regulatory framework linking noncoding genetic variation to MASLD pathogenesis.
Hannah H. Kim, Ellen Y. Zhang, Flavio R. Palma, Aayush Kant, Jose Angel Martinez-Sarmiento, Zixian Guo, Robert L. Mauck, Vivek Shenoy, Marcelo G. Bonini, Su Chin Heo & Melike Lakadamyali. O-SNAP uncovers nanoscale chromatin remodeling in dedifferentiation and stress responses. Nat Commun (2026). https://doi.org/10.1038/s41467-026-73784-9.
Abstract
The multi-scale organization of chromatin underlies gene regulation and cell identity, yet how nuclear architecture remodels during cell state transitions remains poorly understood. Here, we use single-molecule localization microscopy and a comprehensive analytical framework we call O-SNAP to reveal distinct chromatin remodeling trajectories in two biological contexts: dedifferentiation in chondrocytes and nuclear oxidative stress-induced remodeling in mammary epithelial cells. Conventional analyses of single-molecule localization microscopy chromatin images based on qualitative inspection or simple metrics, such as chromatin domain size, fail to capture the subtle chromatin transitions in both contexts. In contrast, O-SNAP quantitatively integrates and compares 144 spatial features extracted from single-molecule localization microscopy data, allowing machine-learning based classification of nuclear states and systematic downstream analyses such as feature selection, volcano plots, and feature set enrichment analysis to determine which spatial features most strongly drive classification results. Our analysis shows that in chondrocytes, in vitro passaging drives heterochromatin formation at late passages, whereas intermediate passages exhibit heterogeneous chromatin remodeling. In contrast, in mammary epithelial cells, nuclear oxidative stress leads to chromatin decompaction specifically in cells overexpressing the oxidation-sensitive histone H3.1 variant. Together, these findings demonstrate that integrated, multiscale spatial features of chromatin are sufficient to robustly discriminate distinct cellular states.
Ashley Karnay, Richardo Linares-Saldana, Qiaohong Wang, Zachary Gardner, Jialiu A Liano, Garrett T Santini, Krishna Kumar Haridhasapavalan, Son C Nguyen, Siewert Hugelier, Bhavana Shewale, Masato T Kanemaki, Jill S Napierala, Marek Napierala, Robert B Wilson, Nicole Dubois, Andrey Poleshko, Wonho Kim, Parisha P Shah, Melike Lakadamyali, Eric F Joyce, Rajan Jain. Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich’s ataxia. Mol Cell. 2026 May 12:S1097-2765(26)00273-X. doi: 10.1016/j.molcel.2026.04.019. Epub ahead of print. PMID: 42127908.
Ruiyao Zhu, Christian E Loo, Christina M Hurley, Jared B Parker, Rahul M Kohli. Mapping Protein Occupancy on DNA with an Unnatural Cytosine Modification. ACS Chem Biol. 2026 May 14. doi: 10.1021/acschembio.6c00280. Epub ahead of print. PMID: 42134787.
Abstract
The epigenome provides a dynamic layer of gene regulatory control above the static genetic sequence. DNA base modifications are key epigenetic regulators, predominantly found within CpG contexts in mammalian genomes. Working in tandem with these DNA modifications, chromatin-associated proteins and transcription factors further control gene expression. Given the interplay of these factors, concurrent mapping of DNA base modifications with protein-DNA occupancy can greatly aid in interpreting the epigenome. Existing multimodal mapping methods include the use of DNA methyltransferases to mark accessible, protein-unbound DNA in non-CpG contexts. However, such approaches can either confound readouts with native DNA modifications or constrain users to third-generation sequencing approaches. To circumvent these limitations, we explored the possibility of introducing an unnatural DNA base modification, 5-carboxymethylcytosine, as an alternative label for protein occupancy. Here, we report our efforts to rationally engineer non-CpG-specific DNA methyltransferases to take on neomorphic DNA carboxymethyltransferase (CxMTase) activities. We find that DNA carboxymethylation of cytosines in GpC contexts shows broad compatibility with the most widely used epigenetic detection methods and can be used to reliably report on protein occupancy states. Using this approach, we reveal the single-molecule binding patterns of LexA, a master repressor in the bacterial DNA damage (SOS) response, at its self-regulated and endogenously methylated promoter. We thus show that unnatural DNA modifications can uncover novel biological insights and potentiate new approaches to multimodal epigenetic profiling.
Elisabetta Manduchi, Hélène C. Descamps, Jinping Liu, Jonathan Schug, Tong Da,Deeksha Lahori, Hilana El-Mekkoussi, Michelle Lee, Eseye Feleke, Diana Bernstein, Chengyang Liu, Ali Naji, Benjamin Glaser, Klaus H. Kaestner & Dana Avrahami . Epigenetic adaptation of beta cells across lifespan and disease. Nat Metab 8, 941–956 (2026). https://doi.org/10.1038/s42255-026-01495-y
Abstract
Although the prevalence of type 2 diabetes (T2D) increases with age, most adults maintain normoglycaemia despite rising insulin resistance owing to the adaptive capacity of pancreatic beta cells to meet increased metabolic demand. However, persistent insulin resistance can lead to beta cell dysfunction and T2D onset. Here we show the mapping of genome-wide DNA methylation (DNAm) patterns and the epigenomic basis of beta cell adaptations by leveraging cell-type-specific methylome data from the Human Pancreas Analysis Program. In healthy donors, we identify progressive age-related demethylation enriched in cis-regulatory elements at beta cell identity and function genes. By contrast, alpha cells show the opposite trajectory, with subtle, age-related hypermethylation. In T2D beta cells, but not alpha cells, we observed further demethylation compared to healthy controls, underscoring a unique capacity of beta cells to respond to changes in metabolic demand. Together, our findings suggest that DNAm remodelling in healthy beta cells reflects a long-term adaptation to metabolic demand, which, in T2D, is accelerated as part of a compensatory response that ultimately fails under sustained insulin resistance.
Natalie A Trigg, Grace S Lee, Alexis G Leach, Colin C Conine, Epididymal extracellular vesicles harbor and convey mRNA to sperm for transfer to zygotes, Nucleic Acids Research, Volume 54, Issue 7, 24 April 2026, gkag330, https://doi.org/10.1093/nar/gkag330
Abstract
The epididymis plays a critical role in promoting sperm maturation, including remodeling the sperm RNA payload. While small RNAs have been extensively studied in this context, the epididymal contribution to larger sperm RNAs, such as messenger RNAs (mRNAs), remains underexplored. This is largely due to the translational quiescence of mature spermatozoa and the hypothesis that these RNAs are residual by-products of spermatogenesis. Yet, mRNAs carried by sperm have been detected in the zygote, indicating they may act beyond fertilization. However, whether epididymal somatic cells contribute mRNAs to sperm, as they do small RNAs, has not been experimentally examined. Here, we provide a comprehensive analysis of the mRNA landscape of mouse sperm, epithelial cells, and extracellular vesicles (EVs) isolated from the proximal (caput) and distal (cauda) epididymis. Through this analysis and sperm-EV co-incubation experiments, we demonstrate the transfer of mRNAs from epididymal EVs to sperm. Further, through sperm RNA microinjection into zygotes, we uncover gene regulation in the early embryo driven by the introduction of sperm RNAs, specific to >200-nucleotide RNA species. These findings reveal the dynamic mRNA profile of sperm that is delivered to the egg and demonstrate that RNA species beyond small RNAs are capable of influencing preimplantation embryo gene expression.
Tanner M. Tessier, Matthew E.R. Maitland, Maria Kutera, Joseph M. Dybas, Jonathan St-Germain, Cheryl H. Arrowsmith, Dalia Barsyte-Lovejoy, Wei Zhang, Brian Raught, Matthew D. Weitzman. Identification of E3 ligase substrates and PROTAC-induced ubiquitylation sites using proximity-based identification of ubiquitin sites (PrIUS). Commun Biol (2026). https://doi.org/10.1038/s42003-026-09964-6
Abstract
The ubiquitin system regulates virtually all cellular processes, yet the vast majority of ubiquitylation sites identified in the human proteome cannot be attributed to specific E3 ligases. This knowledge gap hampers our understanding of ubiquitin signaling and the development of therapeutics leveraging the ubiquitylation system. Here we present Proximity-based Identification of Ubiquitin Sites (PrIUS), a versatile mass spectrometry-based approach combining proximity-dependent biotinylation (BioID) with ubiquitin remnant (diGly) enrichment. PrIUS enables simultaneous identification of E3 ligase interactors and direct mapping of substrate ubiquitylation sites within a single workflow. Using the E3 ligase NEDD4L, we demonstrated that E3 interactomes are inherently rich for diGly-modified peptides that remain largely undetectable without PTM-specific enrichment. PrIUS identified hundreds of high-confidence ubiquitylation sites, successfully distinguished substrates from non-substrate interactors (including adapters and E2 enzymes), and identified non-degradative ubiquitylation events. We also demonstrate utility for characterizing targeted protein degrader mechanisms by precisely mapping PROTAC-induced ubiquitylation sites. PrIUS thus provides a useful approach for elucidating E3-substrate relationships and characterizing mechanisms for emerging degrader therapeutics at amino acid resolution.
Diqiu Ren, Shangshang Wang, Keisuke Yamada, Yuqiao Liu, Robert Hapke, Aktan Alpsoy, Yugong Ho, Canjing Zhang, Yemin Lan, Shuo Zhang, Joseph P. Milazzo, Ruchi Lohia, Kiara N. Berrios, Yongjun Li, Evan W. Weber, Qin Li, Christopher R. Vakoc, Andy J. Minn, Rahul M. Kohli, Junwei Shi. Inducible, split base editors for in vivo cancer functional genomics. Nat Biotechnol (2026). https://doi.org/10.1038/s41587-026-03077-5
Abstract
Cancer functional genomics using CRISPR base editors (BEs) holds great promise for molecular characterization and new target discovery. However, traditional BEs, using intact DNA deaminases as mutators, are often constrained by limited control and nonspecific toxicities. Here we developed a small-molecule-controllable system using split-engineered BEs (seBEs). By placing deaminase activity under small-molecule control, seBEs significantly reduced cellular toxicity and enabled robust and inducible in vivo functional genomics screens. High-density seBE genetic screens using ~11,000 single guide RNAs in vitro and ~3,700 single guide RNAs in vivo reveal known and previously unknown loss-of-function and dominant-negative mutations in cancer therapeutic targets. A deeper tiling seBE screen against Adar1, a key mediator in cancer immunotherapy, reveals critical residues within functional domains that show no phenotype in vitro but distinctively elicit non-cell-autonomous cancer dependencies in vivo. Overall, our seBE system offers a generalizable, controllable and highly efficient method to systematically identify key residues in cancer functional genomics.
De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion
Nicholas G Aboreden, Han Zhao, Jin H Yang, Fengnian Shan, Fuhai Liu, Anders S Hansen, Haoyue Zhang, Gerd A Blobel. De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion. Nat Genet. 2026 Apr;58(4):881-891. doi: 10.1038/s41588-026-02565-3. Epub 2026 Apr 13. PMID: 41974991.
Abstract
NIPBL promotes chromatin loop extrusion by the cohesin complex until it stalls at convergently oriented CTCF sites, forming structural loops. While a large fraction of loops connecting cis-regulatory elements (CREs) can be maintained in cohesin-depleted cells, whether the loop extrusion process contributes to the de novo establishment of CRE loops remains unclear. To address this question, we characterized the formation of structural and CRE loops in NIPBL-depleted cells during the mitosis-to-G1-phase transition. Structural loop formation was impaired proportionally to loop length. Computational modeling supports these observations, suggesting that NIPBL promotes both cohesin loading and extrusion. Notably, most CRE loops, regardless of length, were established normally upon NIPBL degradation. While a subset of contacts among weak CREs were formed with delayed kinetics in NIPBL-depleted cells, generally gene activation was only mildly impaired. Collectively, our findings suggest that postmitotic establishment of regulatory contacts and gene transcription can occur independently of chromatin loop extrusion.
Phillip Wulfridge, Nathaniel Rell, John Doherty, Kuo-Chen Fang, Michelle Lee Lynskey, Kavitha Sarma. ADNP regulates chromatin architecture and lineage fidelity during neural differentiation. PLoS Genet. 2026 Apr 1;22(4):e1012081. doi: 10.1371/journal.pgen.1012081. PMID: 41920822; PMCID: PMC13061322.
Abstract
Transition from a pluripotent to a differentiated cell state is accompanied by significant changes in genome organization. Activity dependent neuroprotective protein (ADNP) is a chromatin regulator with critical roles in neurodevelopment and limits the genomic occupancy of CTCF, a master architectural protein in genome organization, in embryonic stem cells. However, ADNP localization, function, and relationship with CTCF in differentiated neural lineages are not well studied. Here we develop a dual degron model which allows us to acutely deplete ADNP in neural progenitor cells (NPCs). We find that ADNP depletion does not impact NPC survival in the short term, but results in a genome organization switch, which favors the formation of short-range chromatin looping interactions coinciding with CTCF accumulation. Furthermore, ADNP localizes to active gene promoters in NPCs that are unoccupied by CTCF, where it prevents over-expression of genes that are activated upon neurodifferentiation and represses those involved in commitment to other lineages. Our findings uncover CTCF-dependent as well as CTCF-independent regulatory mechanisms of ADNP in NPC-specific chromatin organization and gene expression programs that may underlie its essential function in neurodevelopment.
Nicholas S. Galambos, Olivia J. Crocker, Blair K. Schneider, Kennelly S. Allerton, Katrin E. Gross, Alexandra E. Schneider, Jared Lynch, Onur Yukselen, Alper Kucukural, Colin C. Conine. tRNA-derived RNA processing in sperm transmits non-genetically inherited phenotypes to offspring in C. elegans. Nat Commun. 2026 Mar 15. doi: 10.1038/s41467-026-70029-7. Epub ahead of print. PMID: 41833931.
Abstract
The environment encountered by an organism can modulate epigenetic information in gametes to transmit non-genetically inherited phenotypes to offspring. In mouse models, the diet of males regulates specific tRNA-derived RNAs (tDRs) in sperm. After fertilization, tDRs regulate embryonic gene expression and generate metabolic phenotypes in adult offspring through uncharacterized changes during development. Here we demonstrate that in C. elegans, tDRs also accumulate in sperm and similarly transmit epigenetically inherited phenotypes to offspring. We identify the RNaseT2 enzyme, rnst-2, as a regulator of C. elegans tDR accumulation. RNST-2 processes or degrades tRNA-halves, to short <30 nt fragments. This rnst-2 dependent regulation of tDR length distribution modulates specific tDRs in sperm which, after fertilization, regulate early embryonic and developmental gene expression, leading to adaptive phenotypes in progeny. Our findings establish tDRs as a conserved carrier of intergenerational epigenetic information and position the worm as a model for dissecting paternal non-genetic inheritance mechanistically.
Tanner M Tessier, Matthew E R Maitland, Maria Kutera, Joseph M Dybas, Jonathan St-Germain, Cheryl H Arrowsmith, Dalia Barsyte-Lovejoy, Wei Zhang, Brian Raught, Matthew D Weitzman. Identification of E3 ligase substrates and PROTAC-induced ubiquitylation sites using proximity-based identification of ubiquitin sites (PrIUS). Commun Biol. 2026 Apr 9. doi: 10.1038/s42003-026-09964-6. Epub ahead of print. PMID: 41957433.
Abstract
The ubiquitin system regulates virtually all cellular processes, yet the vast majority of ubiquitylation sites identified in the human proteome cannot be attributed to specific E3 ligases. This knowledge gap hampers our understanding of ubiquitin signaling and the development of therapeutics leveraging the ubiquitylation system. Here we present Proximity-based Identification of Ubiquitin Sites (PrIUS), a versatile mass spectrometry-based approach combining proximity-dependent biotinylation (BioID) with ubiquitin remnant (diGly) enrichment. PrIUS enables simultaneous identification of E3 ligase interactors and direct mapping of substrate ubiquitylation sites within a single workflow. Using the E3 ligase NEDD4L, we demonstrated that E3 interactomes are inherently rich for diGly-modified peptides that remain largely undetectable without PTM-specific enrichment. PrIUS identified hundreds of high-confidence ubiquitylation sites, successfully distinguished substrates from non-substrate interactors (including adapters and E2 enzymes), and identified non-degradative ubiquitylation events. We also demonstrate utility for characterizing targeted protein degrader mechanisms by precisely mapping PROTAC-induced ubiquitylation sites. PrIUS thus provides a useful approach for elucidating E3-substrate relationships and characterizing mechanisms for emerging degrader therapeutics at amino acid resolution.
Apratim Mukherjee, Manya Kapoor, Kareena Shankta, Samantha Fallacaro, Raymond D Carter, Gabriela Hayward-Lara, Puttachai Ratchasanmuang, Yara I Haloush, Mustafa Mir. A single cluster of RNA Polymerase II molecules is stably associated with active genes. Nat Commun. 2026 Mar 20;17(1):2580. doi: 10.1038/s41467-026-70775-8. PMID: 41862494; PMCID: PMC13004947.
Abstract
In eukaryotic nuclei, transcription is associated with the clustering of RNA Polymerase II (RNAPII) molecules. The mechanisms underlying cluster formation, their interactions with genes, and their impact on transcriptional activity remain heavily debated. Here, we take advantage of the naturally occurring increase in transcriptional activity during Zygotic Genome Activation (ZGA) in Drosophila melanogaster embryos to characterize the functional roles of RNAPII clusters in a developmental context. Using single-molecule tracking and lattice light-sheet microscopy, we find that RNAPII cluster formation depends on transcription initiation and that cluster lifetimes depend on transcriptional activity when not constrained by interphase duration. We show that single clusters are stably associated with active gene loci during transcription and that cluster intensities are strongly correlated with transcriptional output. Collectively, our data and simulations on cluster formation kinetics show that RNAPII clusters reflect local accumulations of transcriptionally engaged polymerases and do not form through higher-order mechanisms such as phase separation.
The cytoskeleton contributes to abnormal genome-lamina interactions in LMNA-deficient cardiomyocytes
Kaitlyn M Shen, Emily J Shields, Vasia Barka, Ashley Karnay, Leonie M Kurzlechner, Jennifer D Yang, Qiaohong Wang, Benjamin W Lee, Carmen Suay-Corredera, Son C Nguyen, Eric F Joyce, Kenneth B Margulies, Benjamin L Prosser, Parisha P Shah, Rajan Jain. The cytoskeleton contributes to abnormal genome-lamina interactions in LMNA-deficient cardiomyocytes. J Cell Biol. 2026 May 4;225(5):e202506137. doi: 10.1083/jcb.202506137. Epub 2026 Mar 27. PMID: 41891953.
Abstract
The spatial organization of chromatin at the nuclear lamina contributes to genome structure and gene regulation. Mechanical inputs are increasingly recognized as key regulators of nuclear architecture, and understanding how they control genome-lamina interactions and influence diseases associated with the nuclear lamina remains unclear. To understand the role of lamin proteins and the cytoskeleton in peripheral chromatin organization and consider this role in the context of laminopathies, we performed siRNA-mediated partial knockdown of lamin A/C (LMNA) in human cardiomyocytes and examined lamina-associated domains (LADs). Genome-wide mapping and locus-specific imaging reveal that LADs with a distinct molecular signature are preferentially vulnerable to LMNA reduction. A subset of these sensitive LADs retain lamina association when the linker of nucleoskeleton and cytoskeleton complex (LINC) is disrupted or microtubules are depolymerized. These findings indicate that, in the context of a compromised nuclear lamina, cytoskeletal inputs transmitted through the LINC complex play a key role in the reorganization of peripheral chromatin.
Diana Fulmer, Emily J. Shields, Andrey Poleshko, Jonathan A. Epstein. Reorganization of H3K9me2-modified chromatin regions during mouse embryonic development. Dev Biol. 2025 Dec;528:188-203. doi: 10.1016/j.ydbio.2025.09.005. Epub 2025 Sep 17. PMID: 40972967.
Highlights
- H3K9me2-only domains (KODs) are genomic regions that are enriched for enhancers.
- KODs rearrange during embryonic development to adopt cell type-specific configurations.
- Loss of H3K9me2 at enhancers within KODs correlates with gene expression.
- KODs mark regulatory regions with distal enhancers spanning hundreds of kilobases.
Jingxin Li, Pavithran T. Ravindran, Aoife O’Farrell, Gianna T. Busch, Ryan H. Boe, Zijian Niu, Sean Woo, Margaret C. Dunagin, Naveen Jain, Yogesh Goyal, Kavitha Sarma, Meenhard Herlyn, Arjun Raj. AP-1 mediates cellular adaptation and memory formation. Nat Commun (2026). https://doi.org/10.1038/s41467-026-70862-w
Abstract
Cellular responses to environmental stimuli are typically thought to be governed by genetically encoded programs. We demonstrate that cancer cells can form and maintain cellular memories when becoming drug resistant, exhibiting characteristics of cellular learning that are dependent on the transcription factor AP-1. We show that cells exposed to a low dose of therapy adapt to become resistant to a high dose, demonstrating that cells can adapt during this time of stress. The application of therapy itself results in the encoding of transient gene expression into cellular memory and that this encoding occurs for both transiently induced and probabilistically arising expression. Chromatin accessibility shows concomitant persistence. A two-color AP-1 reporter system shows that these memories are encoded in cis, constituting an example of activating cis epigenetics. Our findings establish the formation and maintenance of cellular memories as a critical aspect of gene regulation during the development of therapy resistance.
Christian E Loo, Jared B Parker, Aleksia Barka, Ruiyao Zhu, Matthew R Schnell, Rosella G Cuomo, Heqiao Zhu, Laura Liu, Ashley Chen, Jasleen Gill, Wanding Zhou, Rahul Kohli. Unnatural Cytosine Analogs Potentiate a Customizable, Enzymatic Method for Integrated Epigenetic and Four-Base Genetic Sequencing. J Am Chem Soc. 2026 Mar 11. doi: 10.1021/jacs.5c18450. Epub ahead of print. PMID: 41812666.
Abstract
The interplay of genetic and epigenetic information shapes cell identity, development, and disease. However, standard methods for profiling DNA modifications (e.g., bisulfite sequencing) rely on selective C-to-T conversions, hindering the simultaneous examination of both genetic and epigenetic information. Here, we introduce Integrated Sequencing, which provides high-fidelity mapping of DNA modifications while preserving the native four-base genetic code in single DNA molecules. Integrated-Seq leverages the synthesis of a tethered copy strand with unnatural cytosine analogs that resist enzymatic conversion, combined with a novel DNA deaminase-helicase fusion that drives selective C-to-T conversion of natural cytosines in the original template strand. We demonstrate that Integrated-Seq is compatible with customizable enzymatic readouts to parse 5-methylcytosine and 5-hydroxymethylcytosine, and that preservation of the original four-base genetic code markedly improved enrichment, facilitating analysis of targeted genomic regions. Integrated-Seq thus provides a platform for simultaneous genetic and epigenetic analyses, paving the way for deep insights into fundamental biology and next-generation diagnostics.
Nina Kuprasertkul, Alyssa F Moore, Carina A D’souza, Julia Chini, Eun-Kyung Ko, Sijia Huang, Shuo Zhang, Ashley S Anderson, Shaun Egolf, Laura V Pinheiro, Alison Jaccard, Claudia T Magahis, Lydia Bao, Yann Aubert, Cyria R Olingou, Stephen M Prouty, Donna Brennan-Crispi, David A Hill, John T Seykora, Kathryn E Wellen, Brian C Capell. Inhibiting LSD1 unlocks retinoid AP-1 programming to activate epithelial immunity and skin tumor suppression. J Clin Invest. 2026 Mar 12:e189044. doi: 10.1172/JCI189044. Epub ahead of print. PMID: 41817619.
Abstract
Lysine-specific demethylase 1 (LSD1; KDM1A) orchestrates context-dependent chromatin programs, yet its role in epithelial immunity remains largely unknown. Here, we identify LSD1 as a central brake on retinoid- and AP-1-driven enhancer activation in epidermis and demonstrate that its inhibition induces anti-tumor immunity. While epidermal LSD1 is required during development, acute loss or topical inhibition in adult skin is tolerated and triggers coordinated expression of retinoic acid signaling, lipid remodeling, and chemokine induction pathways. CUT&RUN profiling reveals that LSD1 occupies enhancer regions enriched for AP-1 motifs at retinoid metabolism, lipid homeostasis, and immune genes. LSD1 loss increases H3K4me1/2 and gene activation at these sites, licensing a poised AP-1-retinoid program. Single-cell spatial analyses show that discrete keratinocyte subsets initiate retinoid signaling to recruit dendritic cells and activate CD4+ T cell responses. Topical LSD1 inhibition suppresses cutaneous squamous cell carcinoma in two models while amplifying keratinocyte-immune crosstalk. Functional perturbations reveal that retinoid signaling partially contributes, whereas CD4+ T cells are essential for tumor control. These findings define LSD1 as a master repressor of epithelial immune competence and nominate LSD1 inhibition as a therapeutic strategy to activate retinoid-AP-1 enhancer circuits and drive CD4-dependent tumor immunity in skin cancer.
Guoli Zhu, Galina Rozenberg, Deeksha Lahori, Jonathan Schug, Mark Tigue, Lan Cheng, Kirill Batmanov, Klaus H Kaestner. Villification of the intestinal epithelium is driven by Foxl1 through activation of PDGFRα and BMPs. Nat Commun. 2026 Feb 24. doi: 10.1038/s41467-026-69791-5. Epub ahead of print. PMID: 41735288.
Abstract
The primitive gut tube of mammals initially forms as a simple cylinder consisting of the endoderm-derived, pseudostratified epithelium and the mesoderm-derived surrounding mesenchyme. During mid-gestation, a dramatic transformation occurs in which the epithelium is both restructured into its final cuboidal form and simultaneously folded and refolded to create intestinal villi and intervillus regions. Here, we show that the mesenchymal winged helix transcription factor Foxl1, itself induced by epithelial hedgehog signaling, controls villification by activating BMP and PDGFRα and the planar cell polarity factor Fat4 in epithelial-adjacent telocyte progenitors either directly or indirectly. In the absence of Foxl1-dependent mesenchymal signaling, villus formation and the separation of epithelial cells into mitotic intervillus and postmitotic villus are delayed, and the differentiation of secretory progenitors temporarily blocked. Thus, Foxl1 orchestrates key events during the epithelial transition of the fetal mammalian gut.
Zhendong Cao, Sixiang Yu, Jacqueline Peng, Declan R Barrett, Yuqiao Liu, Jonathan H. Sussman, Changya Chen, Anusha Thadi, Li Liu, Fatemeh Alikarami, Jason Xu, Martin P. Carroll, Kai Tan, Kathrin M. Bernt, Junwei Shi. CRISPR-based functional genomics for dissecting therapeutic dependency in primary acute myeloid leukemia samples. Mol Cell. 2026 Feb 26:S1097-2765(26)00098-5. doi: 10.1016/j.molcel.2026.02.003. Epub ahead of print. PMID: 41759529.
Abstract
Cancer functional genomics enables high-throughput target discovery and mechanistic investigation, yet its application has remained largely confined to mouse models and established human cancer cell lines. Direct functional interrogation of heterogeneous primary tumors offers a powerful opportunity to evaluate therapeutic targets and uncover cancer dependencies or resistance mechanisms. Here, we developed an optimized CRISPR-based platform for functional genomics in patient-derived xenograft and primary acute myeloid leukemia (AML) samples harboring diverse pathogenic mutations. Integrated in vitro and in vivo CRISPR-Cas9 knockout and CRISPR interference (CRISPRi) dropout screens validated known AML-biased targets and identified cis-regulatory elements essential for leukemic growth. Coupling pooled CRISPR perturbations with single-cell RNA sequencing (Perturb-seq) further resolved the perturbation-induced alterations in regulatory networks, cell cycle states, and cellular hierarchies in primary AML samples. Together, these studies establish a general and robust framework for leveraging CRISPR-based functional genomics to directly dissect cancer dependencies and cellular heterogeneity in primary AML patient samples.
Gabor Egervari, Desi C Alexander, Hua Huang, Greg Donahue, Connor Hogan, Mariel Mendoza, Hong Xu, Virginia Lee, Ben Garcia, Nancy Bonini, Shelley Berger. Multiomic single nuclei profiling the mouse hippocampus reveals that ACSS2 confers neuronal resilience to tauopathy. Alzheimers Dement. 2026 Feb;22(2):e70998. doi: 10.1002/alz.70998. PMID: 41685522; PMCID: PMC12902802.
Abstract
Introduction: Epigenomic dysregulation contributes to Alzheimer’s disease (AD) and related tauopathies. Acetyl-CoA synthetase 2 (ACSS2), a nuclear-localized metabolic enzyme in neurons, supports histone acetylation and learning-related gene expression. We examined how ACSS2 loss affects molecular and behavioral phenotypes in a mouse model of tauopathy.
Methods: We induced tauopathy in ACSS2 knockout and control mice via injection of pathological human tau. We assessed transcriptomic, epigenomic, and behavioral changes, and tested long-term acetate supplementation as a rescue strategy.
Results: ACSS2 loss worsened tau-seeding-related phenotypes, particularly in hippocampal pyramidal neurons and Cajal-Retzius cells. Acetate supplementation rescued learning in an ACSS2-dependent manner and restored gene expression linked to cognition.
Discussion: ACSS2 acts as a neuroprotective metabolic enzyme in vulnerable hippocampal neurons, and targeting this pathway through dietary supplementation may offer therapeutic potential for AD and related tauopathies.
Highlights: We combine tau seeding with deletion of acetyl-CoA synthetase 2 (ACSS2) to test this enzyme in an Alzheimer’s disease model. Loss of ACSS2 exacerbates transcriptional and behavioral responses to tau injection. We observe robust transcriptional dysregulation in pyramidal neurons in the hippocampus. We observe reduced numbers of reelin-producing Cajal-Retzius cells in the hippocampus. Acetate supplementation rescues transcriptional and behavioral responses to tau.
Wonho Kim, Daniel S. Park, Son C. Nguyen, Rachel Yang, Eric F. Joyce, Rajan Jain. A genetic screen for modifiers of cohesin clustering identifies regulators of genome folding. Sci Adv. 2026 Jan 30;12(5):eadx5130. doi: 10.1126/sciadv.adx5130. Epub 2026 Jan 30. PMID: 41616049; PMCID: PMC12857682.
Abstract
The cohesin complex orchestrates 3D genome architecture through multiple steps including loading onto chromatin, DNA loop extrusion, stalling of extrusion, and unloading off chromatin. However, the upstream regulatory factors modulating these steps remain largely unexplored. Previous studies suggest that cohesin clustering correlates with its chromatin residence time and loop extrusion activity. Here, we developed, optimized, and performed an imaging-based genetic screen leveraging modulation of cohesin clustering to identify cohesin regulators. Using a sensitized background in which the cohesin unloader WAPL is partially degraded, we screened the druggable genome for effects on cohesin clustering. Through multiple rounds of screening and experimentation, we identified 7 enhancers and 10 suppressors of cohesin clustering. Several factors control genome folding at multiple loci and cohesin loading. Notably, our screen identified factors in mitochondrial function and epigenetic silencing, implicating these processes in the regulation of cohesin activity. This study offers a valuable resource identifying cohesin regulators and provides insights into upstream mechanisms governing genome folding.
Andrew Katznelson, Jingchao Zhang, Greg Donahue, Kenneth S Zaret. Basis for lineage-determining pioneer factors targeting distinct repressed chromatin states. Sci Adv. 2026 Jan 9;12(2):eadz7409. doi: 10.1126/sciadv.adz7409. Epub 2026 Jan 9. PMID: 41512071; PMCID: PMC12787584.
Abstract
Pioneer transcription factors target transcriptionally silent chromatin, thereby enabling gene activation in development, regeneration, and cell reprogramming. However, silent chromatin is heterogeneous, varying in nucleosome stability, nucleosome compaction, and repressive histone modifications, and how pioneer factors may differentially overcome these different chromatin barriers is unknown. We systematically compared the chromatin targeting of 13 embryonic transcription factors and found that the DNA binding domain (DBD) type predicts whether a pioneer factor targets low-turnover nucleosomes in compact chromatin, dynamic nucleosomes in compact chromatin or functions as a nonpioneer factor targeting accessible chromatin. By contrast, non-DBD domains enable targeting of repressed chromatin marked by H3K9me3 or H3K27me3. Fusions of different non-DBD segments of heterochromatin-targeting pioneer factors to the transcription factor SOX2 can expand binding of SOX2 target motifs within heterochromatin and improve cellular reprogramming. Our study unveils how different forms of silent chromatin are coordinately targeted by lineage-specifying factors.
Sean Louzon, Emily Feierman, Qi Qiu, Marissa J Maroni, Camille N Quaye, Roxanne Perez-Tremble, Hao Wu, Erica Korb. Age- and cell-type-specific effects of histone variant H2BE in the brain. Cell Rep. 2025 Dec 23;44(12):116655. doi: 10.1016/j.celrep.2025.116655. Epub 2025 Dec 9. PMID: 41379615.
Abstract
Transcription is regulated in part through histone proteins. Histones can be replaced with variant forms that are particularly critical in the brain and accumulate throughout the lifespan. Recent findings demonstrated that the histone variant H2BE regulates chromatin structure, neuronal transcription, and mouse behavior. However, the role of H2BE in other cell types and throughout the lifespan remains unknown. Here, we discovered that H2BE is enriched in astrocytes and accumulates with age in both astrocytes and neurons. Further, we found that H2BE promotes synaptic gene expression in young neurons and astrocytes and is critical in both cell types for proper synaptic function. In aging brains, loss of H2BE similarly affects synaptic genes in neurons but dampens age-related transcriptional changes in both astrocytes and neurons. Lastly, H2BE loss disrupts long-term memory but improves working memory in aging mice. Together, these data link histone variants with aging-related gene-expression changes in both astrocytes and neurons.
Emily R Feierman, Alekh Paranjapye, Annabel K Sangree, Rili Ahmad, Marissa J Maroni, Qi Qiu, Kyuhyun Choi, Marc Fuccillo, Hao Wu, Erica Korb. Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling. Cell Rep. 2025 Dec 19;45(1):116694. doi: 10.1016/j.celrep.2025.116694. PMID: 41422507.
Abstract
Neuronal responses to stimuli rely on transcriptional programs controlled by histone proteins, including histone variants. Recent findings demonstrate that the variant H2BE promotes transcription and is critical for long-term memory, which relies on intact activity-dependent responses. However, whether H2BE is regulated by synaptic stimuli and controls activity-dependent responses remains to be determined. Here, we demonstrate that, unlike other variants, H2BE is depleted following long-term but not short-term increases in activity, indicating that its loss may promote homeostatic downscaling. Neurons lacking H2BE are unable to mount proper long-term activity-dependent transcriptional responses both in cultured neurons and in animal models. Lastly, we demonstrate that H2BE-knockout neurons fail to undergo the electrophysiological changes associated with homeostatic plasticity. In summary, these data demonstrate that H2BE expression is inversely correlated with activity and is necessary for long-term activity-dependent scaling responses, revealing a mechanism through which histone variants control homeostatic plasticity in neurons.
Elizabeth A Traxler, Quynn Hotan, Yue Shao, Chad Komar, Qingzhou Chen, Megan S Saari, A Josephine Thrasher, Shuchen Yang, Kunhua Qin, Michelle Wang, Scott A Peslak, Osheiza Abdulmalik, Belinda M Giardine, Cheryl A Keller, Ross C Hardison, Andy J Minn, Eugene Khandros, Junwei Shi, Gerd A Blobel. Optimized CRISPR-Cas12a genome-wide screen reveals PTPA phosphatase pathway in fetal hemoglobin silencing. Blood. 2026 Jan 12:blood.2025030137. doi: 10.1182/blood.2025030137. PMID: 41525452.
Abstract
Reactivating the fetal globin genes HBG1 and HBG2 in adult erythroid cells represents a validated therapeutic approach for hemoglobinopathies. Central mediators of the fetal-to-adult hemoglobin transition include the direct transcriptional HBG1/2 repressors BCL11A1,2, LRF3, and NFIA/X4. Limited-scale screens have attempted to expand the regulatory circuity surrounding fetal globin silencing, but systematic genome-wide dissection of such pathways is lacking. We employed a two-tiered genetic screening strategy – a novel CRISPR-Cas12a-based screening platform followed by a domain-focused CRISPR-Cas9 screen – to interrogate all known human coding genes for their impact on HBG1/2 regulation and erythroid cellular fitness, generating a comprehensive resource for the field. Among the top hits was PTPA, an activator of the serine-threonine phosphatase PP2A whose loss elevates HBG1/2 levels while preserving erythroid differentiation. Phenotypic rescue experiments revealed that PTPA silences HBG1/2 expression primarily by regulating BCL11A expression. To our knowledge, this study represents the most comprehensive CRISPR dissection of HBG regulation to date, highlighting the power of Cas12a-based genome-scale screening for uncovering disease-relevant pathways.
Tian Huang, Charles Hodgens, Sandhan Prakash, Marco Marconi, Krzysztof Wabnik, Rosangela Sozzani, Doris Wagner. A negative feedback loop between TERMINAL FLOWER1 and LEAFY protects inflorescence indeterminacy. Science. 2026 Jan 22:eadv5429. doi: 10.1126/science.adv5429. PMID: 41570111.
Abstract
Inflorescences of flowering plants adopt diverse genetically programmed and environmentally tuned architectures. By contrast, continued maintenance of the stem-cell pool within the apical meristem is unresponsive to environmental cues. Through a combination of modeling and experimentation in Arabidopsis, we reveal a negative feedback loop that buffers environmental signals. This loop comprises the determinacy-promoting pioneer transcription factor LEAFY (LFY) and the indeterminacy-promoting transcriptional co-repressor TERMINAL FLOWER1 (TFL1). At the transition to the flower-producing reproductive phase, LFY directly and quantitatively up-regulates expression of TFL1. TFL1 in turn negatively feeds back on LFY to prevent LFY overaccumulation. This blocks inflorescence termination even under strong florally inductive signals. Our work uncovers a mechanism for robust environmental buffering involving differential responses of two cell populations to the same environmental stimulus.
Yeqiao Zhou, Atishay Jay, Noah Burget, Tobias Friedrich, Sora Yoon, Jessica Alsing, Guy Nir, Rudolf Grosschedl, Golnaz Vahedi, Robert B. Faryabi. Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation. Nat Cell Biol. 2025 Dec 2. doi: 10.1038/s41556-025-01827-2. PMID: 41331087.
Abstract
Multiple enhancers, often separated by vast genomic distances, regulate key genes. However, how the folding of individual chromatin fibres enables cell-type-restricted multi-enhancer regulation remains unclear. Here, using acute protein degradation and time-resolved chromatin conformation capture in mantle cell lymphoma, we found that the B cell-lineage-determining factor EBF1 organizes multiple enhancers around sparsely distributed genes essential for B cell identity and oncogenesis. Time-resolved sub-diffraction optical tracing of more than 100,000 chromatin fibres further revealed diverse topological conformations that facilitate multi-enhancer interactions. Mechanistically, we discovered that enhancer positioning at local topological centres is required for promoter engagement, with EBF1 acting as a permeable barrier to loop-extruding cohesin at enhancers. Extending these findings to T cell leukaemia, we show that lineage-determining transcription factors such as EBF1 and TCF1 radially position enhancers within gene loci to enable multi-enhancer regulation of key oncogenes at the single-allele level.
Michael D. Murphy, Keegan S. Krick, Shuo Zhang, Elizabeth AHeller. Corticosterone accelerates behavioral inflexibility via plasticity-related gene expression in the dorsal striatum. Neuropsychopharmacology. 2025 Dec 9. doi: 10.1038/s41386-025-02293-y. PMID: 41366066.
Abstract
Behavioral flexibility allows organisms to modify actions based on new information, such as shifts in reward value or availability, and is promoted by the dorsomedial striatum (DMS). In contrast, behavioral inflexibility provides efficiency and automaticity in familiar contexts, and is promoted by the dorsolateral striatum (DLS). Importantly, chronic elevation of the primary stress hormone, corticosterone (CORT) in rodents or cortisol in humans, impairs behavioral flexibility through dendritic atrophy in the DMS, and promotes inflexible behavioral response strategies through dendritic outgrowth in the DLS. However, understanding of changes in gene expression underlying behavioral inflexibility is lacking. We used a food-motivated operant task in male and female mice to define gene changes that accompany the shift to inflexible behavior with CORT. We discovered that CORT-accelerated loss of behavioral flexibility is accompanied by decreased DMS- and increased DLS-specific synaptic plasticity gene expression, and that distinct genes are either differentially expressed or spliced in the transition to inflexible behavior. Splicing analysis suggests that repressed activity in the DMS during the transition to inflexible behavior may reflect both reduced expression and increased degradation of plasticity-related mRNA transcripts. Finally, given the ability of CORT to influence histone acetylation, we defined CORT-mediated H3K9ac enrichment profiles associated with synaptic plasticity gene regulation stratified by sex and striatal subregion. This study is the first to define CORT-driven epigenetic regulation in the DMS and DLS during the CORT-accelerated transition from flexible to inflexible behavior in male and female mice.
Sung-Ya Lin, Hannah R. Futeran, Briana N. Cruga, Andrew Santiago-Frangos, Mia T. Levine. Rapid compensatory evolution within a multiprotein complex preserves telomere integrity. Science. 2025 Nov 27;390(6776):918-924. doi: 10.1126/science.adv0657. Epub 2025 Nov 27. PMID: 41308135.
Abstract
Intragenomic conflict with selfish genetic elements spurs adaptive changes in subunits of essential multiprotein complexes. Whether and how these adaptive changes disrupt interactions within such complexes and threaten their essential functions remains unexplored. To investigate this, we exploited a Drosophila melanogaster multiprotein complex that protects telomeres from lethal fusions despite one subunit, HOAP (HP1/ORC-associated protein), evolving adaptively to restrict selfish telomeric retrotransposons. Swapping HOAP’s adaptively evolving interaction partner, HipHop (HP1-HOAP-interacting protein), between closely related Drosophila species disrupted HOAP recruitment to the telomere, leading to lethal telomere fusions. Reverting six adaptively evolving sites on HipHop’s interaction surface with HOAP, or introducing its conspecific HOAP, restored protein recruitment, telomere protection, and viability. Our in vivo, evolution-guided manipulations illuminate how intermolecular compensatory evolution preserves essential functions in the face of antagonism by selfish elements.
Yeqiao Zhou, Yimin Sheng, Dongbo Hu, Atishay Jay, Golnaz Vahedi, Robert B. Faryabi. OLIVE provides rapid visualization and analysis of chromatin tracing experiments. Cell Rep Methods. 2025 Nov 17;5(11):101209. doi: 10.1016/j.crmeth.2025.101209. Epub 2025 Oct 20. PMID: 41118766; PMCID: PMC12664882.
Abstract
Optical chromatin tracing experiments directly capture the three-dimensional folding of thousands of individual alleles, highlighting the need for a tool that enables fast, interactive, and analytical browsing of such data. Here, we introduce optical looping interactive viewing engine (OLIVE), the first web-based application designed for high-throughput ball-and-stick chromatin tracing data studies that functions similarly to genome browsers. OLIVE allows users, regardless of computational expertise, to input their own data for automated reconstruction of chromatin fibers at individual alleles or to browse and analyze annotated publicly available datasets. Using OLIVE’s functionalities, users can interact with three-dimensional presentation of traced alleles and query them based on spatial features, including pairwise distances and perimeters between their segments. Finally, OLIVE calculates and presents several polymer physics metrics of each allele, providing quantitative summaries for hypothesis-driven studies. OLIVE is an open-source project accessible at https://faryabilab.github.io/chromatin-traces-vis/.
Maryam Abedi, Priyadarshini Rai, Yeqiao Zhou, Chengyang Liu, Isabelle Johnson, Aditi Chandra, Maria Fasolino, Susan Rostami, Wei Wang, Zaw Min, Yanjing Li, Ming Yu, Atishay Jay, Vung Lian, Michael Silverman, Klaus H Kaestner, Ali Naji, Robert B Faryabi, Golnaz Vahedi. Joint profiling of gene expression and chromatin accessibility in pancreatic lymph nodes and spleens in human type 1 diabetes. Sci Immunol. 2025 Nov 21;10(113):eadz0472. doi: 10.1126/sciimmunol.adz0472. Epub 2025 Nov 21. PMID: 41270190.
Abstract
Type 1 diabetes (T1D) is an autoimmune disease characterized by the destruction of insulin-producing β cells in the pancreas. While current therapies focus on managing the disease, a deeper understanding of the underlying molecular mechanisms is crucial for developing disease-modifying interventions. In this study, we conducted a comprehensive analysis of gene expression and chromatin accessibility in nearly 1 million immune cells from the pancreatic lymph nodes and spleens of 43 individuals with and without T1D. We found a distinct subset of CD4 T cells specifically present in the pancreatic lymph nodes of organ donors representing the active disease stage. These cells exhibited elevated activity of NFKB1 and BACH2, along with extensive chromatin remodeling associated with these transcription factors, which we also corroborated in a mouse model of T1D. A better understanding of these NFKB1-BACH2-expressing CD4 T cells may lead to therapeutic avenues for preventing or delaying T1D onset.
Adriana N Santiago-Ruiz, Siewert Hugelier, Gabriela L Correa, Charles R Bond, Edward B Lee, Melike Lakadamyali. Morphological and Hyperphosphorylation Transitions of Nanoscale Tau Aggregates in Alzheimer’s Disease. Adv Sci (Weinh). 2025 Nov 19:e09773. doi: 10.1002/advs.202509773. PMID: 41255200.
Abstract
Tau aggregation plays a critical role in Alzheimer’s Disease (AD), where neurofibrillary tangles (NFTs) are a pathological hallmark. While much attention is given to NFTs, emerging evidence highlights nano-sized tau oligomers as toxic entities. Using super-resolution microscopy, we visualized nano-sized tau aggregates (nano-aggregates) in human postmortem brain tissues from intermediate and advanced AD, Primary Age-Related Tauopathy (PART), and controls lacking tau pathology. Surprisingly, tau nano-aggregates hyperphosphorylated at threonine 231 (p-T231) and threonine 181 (p-T181)are detected in control cases, whereas hyperphosphorylated serine 202/threonine 205 (p-S202/T205)nano-aggregates are specifically associated with AD and, to a lesser extent, observed in PART. This finding suggests that distinct hyperphosphorylation signatures distinguish physiological from pathological nano-aggregates. Moreover, nano-aggregates exhibit morphological differences between AD and non-AD conditions, increasing in size and complexity in AD. In advanced AD, nano-aggregates typically contain multiple distinct hyperphosphorylated residues, whereas intermediate AD nano-aggregates are predominantly marked by a single hyperphosphorylated residue. These findings reveal novel transitions in the morphology and hyperphosphorylation states of tau nano-aggregates as they shift from physiological to pathological forms. The ability to detect and profile physiological and pathological nanoscale tau aggregates in human brain tissues opens new avenues for studying the molecular underpinnings of tauopathies.
Abhirup Bagchi, Sindhu Billakanti, Vanessa Shehu, Kathryn M Farrell, Sarah A Cotteta, Bailey N Godfrey, Micaela Alpert, Jacob Flores Zeranski, Krista A Budinich, Zhuangzhuang Geng, Osheiza Abdulmalik, Belinda M Giardine, Cheryl A Keller, Ross C Hardison, Junwei Shi, Eugene Khandros. Highly discriminative globin gene activation by the non-canonical BAF chromatin remodeling complex. Blood. 2025 Nov 14:blood.2025029429. doi: 10.1182/blood.2025029429. PMID: 41237357.
Abstract
The regulation of the switch from fetal (HBG) to adult (HBB and HBD) b-globin gene expression has served as a paradigm for clinically relevant developmental transcriptional control. Mechanistic studies of this switch have predominantly focused on HBG repressors with comparatively little attention paid to potential HBG activators. We found that in adult type HUDEP2 erythroid cells, the ATP-dependent chromatin remodeler BRG1 preferentially activates the HBG genes as well as the minor adult HBD gene. BRG1 is a core catalytic subunit of three BAF complexes, canonical BAF, polybromo BAF, and non-canonical BAF (ncBAF) that regulate chromatin accessibility in distinct gene- and cell-type contexts. To dissect the specific BAF complex configuration mediating selective activation of HBG and HBD in erythroid cells, we performed CRISPR mediated targeting of individual subunits and pinpointed the regulatory activity to the ncBAF complex. Loss of the ncBAF complex subunits BRD9 and BAF60A preferentially decreased HBG and HBD transcription while accelerating terminal erythroid differentiation and hemoglobinization. Acute pharmacologic depletion of BRD9 in HUDEP2 and primary erythroid cells selectively reduced transcription of HBD and HBG, suggesting direct effects at these genes. Collectively, our unexpected findings demonstrate that the BAF complex, through distinct subcomplex configurations, can regulate selective gene expression within a multi-gene cluster. This expands the traditional view of BAF as a general co-activator, highlights its role in gene-specific regulation, and identifies a potential target for therapeutic manipulation of b-like globin genes in erythroid cell disorders.
Sam Reffsin, Jesse Miller, Kasirajan Ayyanathan, Margaret C Dunagin, Yael Heyman, Naveen Jain , David C Schultz, Sara Cherry, Arjun Raj. Single-cell susceptibility to viral infection is driven by variable cell states. Cell. 2025 Nov 14:S0092-8674(25)01193-6. doi: 10.1016/j.cell.2025.10.021. PMID: 41240909.
Abstract
The ability of a virus to infect a cell is partly determined by host factors required for the viral life cycle. However, not every cell of a given type is equally susceptible to infection. Profiling susceptible subsets of cells could reveal additional host factors, but viral infection obscures and remodels the state of these cells prior to infection. We used single-cell clone tracing to retrospectively identify cells that were highly susceptible to infection with SARS-CoV-2. Depletion of certain factors identified by our approach revealed roles in viral entry, whereas others exerted control over the infectable cell state itself. Patient lung samples revealed heterogeneous expression of these factors in vivo, with heightened expression in particular inflammatory pathologies. We further found a distinct cell state that was susceptible to the influenza A virus. Thus, intrinsic variability in state is a major determinant of whether individual cells can be infected by a virus.
David C. Goldberg, Hongxiang Fu, Daniel Atkins, Ethan Moyer, Chin Nien Lee, Yanxiang Deng, Wanding Zhou. KnowYourCG: Facilitating base-level sparse methylome interpretation. Sci. Adv. 11, eadw3027 (2025). DOI:10.1126/sciadv.adw3027
Abstract
Decoding DNA methylomes for biological insights is critical in epigenetics research. We present KnowYourCG (KYCG), a data interpretation framework designed for functional DNA methylation analysis. Unlike existing tools that target genes or genomic intervals, KYCG features direct base-level screenings of diverse biological and technical influences, including sequence motifs, transcription factor binding, histone modifications, replication timing, cell-type–specific methylation, and trait associations. Through implementing efficient infrastructure that rapidly screens and investigates thousands of knowledgebases, KYCG addresses the challenges of data sparsity in various methylation datasets, including low-pass or single-cell DNA methylomes, 5-hydroxymethylation (5hmC) profiles, spatial DNA methylation maps, and array-based datasets for epigenome-wide association studies. Applying KYCG to these datasets provides valuable insights into cell differentiation, cancer origins, epigenome-trait associations, and technical issues such as array artifacts, single-cell batch effects, and Nanopore 5hmC detection accuracy. Our tool simplifies large-scale methylation analysis and integrates seamlessly with standard assay technologies.
Michael C. Tackenberg, Kristina M. Heliodoro, Lily C. Melink, Yifan Liu, Kun Zhu, Mitchell A. Lazar. Normal circadian period length requires repression of Npas2 by REV-ERB nuclear receptors. Cell Reports, Volume 44, Issue 10, 2025, 116437, ISSN 2211-1247, https://doi.org/10.1016/j.celrep.2025.116437 (https://www.sciencedirect.com/science/article/pii/S2211124725012082)
Summary
REV-ERB nuclear receptors are integrated into the molecular circadian clock present in most mammalian cells. Loss of REV-ERBs (REV-ERB DKO) within the suprachiasmatic nucleus (SCN) in vivo leads to a marked shortening of the circadian period, but it remains unclear whether REV-ERB regulation of circadian period is tissue autonomous, if it is conserved across tissues, and how it is established. Here, we show that period shortening in the absence of REV-ERBs is tissue autonomous, is consistent between brain and liver, and is brought about through derepression of clock transcription factors NPAS2 and CLOCK. Thus, in addition to disruption of synchrony with the external environment, our results demonstrate that the circadian impacts of REV-ERB loss also include the alteration of core circadian properties with tissue-specific consequences.
Haidong Yan, John P Mendieta, Xuan Zhang, Ziliang Luo, Alexandre P Marand, Yan Liang, Mark A A Minow, Yun Zhong, Yarong Jin, Hosung Jang, Li X, Xinxin Zhang, Thomas Roulé, Doris Wagner, Xiaoyu Tu, Yonghong Wang, Daiquan Jiang, Silin Zhong, Linkai Huang, Susan R Wessler, Robert J Schmitz. A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution. Nat Plants. 2025 Oct;11(10):2050-2071. doi: 10.1038/s41477-025-02106-6. Epub 2025 Sep 17. PMID: 40962852; PMCID: PMC12537502.
Abstract
Cis-regulatory elements (CREs) are essential for regulating gene expression, yet their evolutionary dynamics in plants remain elusive. Here we constructed a single-cell chromatin accessibility atlas for Oryza sativa from 103,911 nuclei representing 126 cell states across nine organs. Comparative genomics between O. sativa and 57,552 nuclei from four additional grass species (Zea mays, Sorghum bicolor, Panicum miliaceum and Urochloa fusca) revealed that chromatin accessibility conservation varies with cell-type specificity. Epidermal accessible chromatin regions in the leaf were less conserved compared to other cell types, indicating accelerated regulatory evolution in the L1-derived epidermal layer of O. sativa relative to other species. Conserved accessible chromatin regions overlapping the repressive histone modification H3K27me3 were identified as potentially silencer-like CREs, as deleting these regions led to up-regulation of gene expression. This study provides a comprehensive epigenomic resource for the rice community, demonstrating the utility of a comparative genomics approach that highlights the dynamics of plant cell-type-specific CRE evolution.
Eimear Lagan, Dáire Gannon, Ademar Jesus Silva, Peter Bibawi, Anthony M. Doherty, Darragh Nimmo, Rachel McCole, Craig Monger, Giovani Luiz Genesi, Aurelie Vanderlinden, James A. Innes, Charlotte L.E. Jones, Lu Yang, Bryan Chen, Guido van Mierlo, Pascal W.T.C. Jansen, Chinmayi Pednekar, Alexander Von Kriegsheim, Kieran Wynne, Francisco J. Sánchez-Rivera, Yadira M. Soto-Feliciano, Angel M. Carcaboso, Michiel Vermeulen, Giorgio Oliviero, Chun-Wei Chen, Richard E. Phillips, Adrian P. Bracken, Gerard L. Brien. A specific form of cPRC1 containing CBX4 is co-opted to mediate oncogenic gene repression in diffuse midline glioma. Molecular Cell. 2025/06/05. DOI: 10.1016/j.molcel.2025.04.026.
Highlights
- cPRC1 complexes with CBX4 and PCGF4 are essential in H3K27M-mutant DMG
- The altered H3K27me3 landscape in DMG redistributes cPRC1 complexes on chromatin
- CBX4-PCGF4-cPRC1 acts non-redundantly to repress PRC1/2 target genes in DMG
- CBX4’s central region promotes preferential formation of cPRC1 with PCGF4
Summary
Diffuse midline glioma (DMG) is a fatal childhood brain tumor characterized primarily by mutant histone H3 (H3K27M). H3K27M causes a global reduction in Polycomb repressive complex 2 (PRC2)-mediated H3K27 trimethylation (H3K27me3). Paradoxically, PRC2 is essential in DMG cells, although the downstream molecular mechanisms are poorly understood. Here, we have discovered a specific form of canonical PRC1 (cPRC1) containing CBX4 and PCGF4 that drives oncogenic gene repression downstream of H3K27me3 in DMG cells. Via a novel functional region, CBX4 preferentially associates with PCGF4-containing cPRC1. The characteristic H3K27me3 landscape in DMG rewires the distribution of cPRC1 complexes, with CBX4/PCGF4-cPRC1 accumulating at H3K27me3-enriched CpG islands. Despite comprising <5% of cPRC1 in DMG cells, the unique repressive functions of CBX4/PCGF4-cPRC1 are essential for DMG growth. Our findings link the altered distribution of H3K27me3 to imbalanced cPRC1 function, which drives oncogenic gene repression in DMG, highlighting potential therapeutic opportunities for this incurable childhood brain cancer.
Sol Moe Lee, David C. Goldberg, Cameron Cloud, Jared B. Parker, Christopher Krapp, Christian E. Loo, Elliot Kim, Ivan Zhao, Chengcheng Jin, Rishi Porecha, Marisa S. Bartolomei, Rahul M. Kohli, Wanding Zhou.. A ternary-code DNA methylome atlas of mouse tissues. Genome Biol 26, 343 (2025). https://doi.org/10.1186/s13059-025-03808-y
Abstract
Background
DNA cytosine modifications, including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), are key epigenetic regulators with distinct functions. Dissecting the ternary code (C, 5mC, 5hmC) across tissues and cell types remains a critical priority due to the limitations of traditional profiling methods based on bisulfite conversion.
Results
Here, we leverage the combined bisulfite and enzymatic (bACE) conversion with the Mouse Methylation BeadChip to generate 265 base-resolution ternary-code modification maps of 5mC and 5hmC across 29 mouse tissue types spanning 8–76 weeks of age and both sexes. Our atlas reveals a complex grammar of 5hmC distribution, jointly shaped by cell mitotic activity, chromatin states, and interplay with 5mC at the same and neighboring CpG sites. Of note, we demonstrate that 5hmC significantly complements 5mC-based biomarkers in delineating cell identity in both brain and non-brain tissues. Each modification state, including 5hmC alone, accurately discriminates tissue types, enabling high-precision machine learning classification of epigenetic identity. Furthermore, the ternary methylome variations extensively implicate gene transcriptional variation, with age-related changes correlated with gene expression in a tissue-dependent manner.
Conclusions
Our work reveals how tissue, sex, and age jointly govern the dynamics of the two cytosine modifications, augments the scope of DNA modification biomarker discovery, and provides a reference atlas to explore epigenetic dynamics in development and disease.
Hyuk-Joon Jeon, Mia T. Levine, Michael A. Lampson. A parent-of-origin effect on embryonic telomere elongation determines telomere length inheritance. Current Biology. 2025/09/25. DOI: https://doi.org/10.1016/j.cub.2025.08.052.
Summary
Telomeres are composed of specialized DNA, RNA, and proteins that interact to preserve the integrity of chromosome termini.1,2 Despite this vital function, telomere length varies dramatically within and between species. Genome-wide association studies have identified multiple genes that explain a portion of this variation,3 suggesting that telomere length is inherited as a classic quantitative trait. However, telomere length is also directly inherited as a DNA sequence. Here, we show that neither the polygenic nor the direct inheritance paradigm fully accounts for telomere length inheritance, which also depends on a parent-of-origin effect on telomere elongation in the early embryo. By reciprocally crossing mouse strains with different telomere lengths, we find that telomeres elongate in hybrid embryos only when maternal telomeres are short and paternal telomeres are long. In the reciprocal cross, telomeres shorten. These differences in embryonic telomere elongation, which emerge before zygotic genome activation, predict observed differences in adult telomere length. Moreover, when telomeres do elongate, we find molecular signatures of a recombination-based mechanism of telomere elongation, called the alternative lengthening of telomeres (ALT) pathway, previously suggested to elongate telomeres in the pre-implantation embryo. We propose that ALT is triggered by a combination of genetic asymmetry in telomere length and epigenetic asymmetry between maternal and paternal chromosomes in the zygote. Our findings offer new insight into the complex interaction of genetic and epigenetic determinants of telomere length inheritance.
Xiaokang Wang, Nicholas G Aboreden, Ying Cai, Jessica C Lam, Kate A Hnederson, Jiaqi Xiang, Belinda M Biardine, Ross C Hardison, Cheryl A Keller, Lalitha Nagarajan, Stephen J Brandt, Gerd A Blobel. Single-stranded DNA-binding proteins are essential components of the architectural LDB1 protein complex. Mol Cell. 2025 Aug 21;85(16):3074-3089.e8. doi: 10.1016/j.molcel.2025.07.012. Epub 2025 Aug 12. PMID: 40803327; PMCID: PMC12402931.
Abstract
Transcriptional enhancers are brought into proximity with promoters via chromatin looping. The architectural transcription cofactor LDB1 facilitates spatial connectivity among enhancers and promoters, but whether this occurs through simple dimerization or requires heterotypic protein assemblies is unknown. Here, we investigated the role of single-stranded DNA-binding proteins (SSBPs) in regulating LDB1-mediated chromatin looping and transcription. SSBP2, SSBP3, and SSBP4 colocalize with LDB1 genome wide. Among these, only SSBP3 is essential for murine erythroid cell viability, LDB1 function, and transcription. LDB1, but not single-stranded DNA, is the predominant genome-wide tether of SSBP3 to chromatin. SSBP3 depletion in SSBP2/4 knockout cells globally weakened LDB1-dependent chromatin loops and lowered nascent transcription without impacting LDB1’s chromatin binding. Chromatin tethering experiments revealed that SSBP3 and LDB1 mutually depend on each other to form looped contacts. SSBP3 stabilizes LDB1 dimerization in vitro, providing a possible mechanism. SSBPs emerge as key functional components of the architectural LDB1 complex.
Joanne L. Thorvaldsen, Aimee M. Juan, Yemin Lan, Christopher Krapp, Marisa S. Bartolomei. Igf2 adult-specific skeletal muscle enhancer activity revealed in mice with intergenic CTCF boundary deletion. PLOS Genetics. 29 August 2025. DOI: https://doi.org/10.1371/journal.pgen.1011834.
Abstract
Precise, monoallelic expression of imprinted genes is governed by cis regulatory elements called imprinting control regions (ICRs) and enhancer-promoter (E-P) interactions shaped by local chromatin architecture. The Igf2/H19 locus employs allele-specific CTCF binding at the ICR to instruct enhancer accessibility to maternal H19 and paternal Igf2 promoters. Here, we investigate the CTCF-bound centrally conserved domain (CCD), intergenic to H19 and Igf2, and an adjacent widely expressed lncRNA. Using transgenic mice, deletion alleles reinforced CCD as a neonatal muscle-specific repressor of maternal Igf2. However, deletion of the abutting lncRNA did not affect Igf2 levels. Unexpectedly, in adult skeletal muscle where Igf2 is normally repressed, absence of CCD resulted in remarkable, high-level activation of Igf2 from both parental alleles. Through multimodal chromatin analyses, we identified a conserved putative adult skeletal muscle enhancer (PaSME) insulated between chromatin domains at ICR and CCD. We propose that removal of CCD allows PaSME to drive robust abnormal Igf2 activation on both alleles in adult skeletal muscle. Thus, we uncover CCD as a developmental biallelic muscle-specific repressor, adding a new layer of architectural regulation to the extensively studied Igf2/H19 locus.
Chin Nien Lee, Hongxiang Fu, Angelysia Cardilla, Wanding Zhou, Yanxiang Deng. Spatial joint profiling of DNA methylome and transcriptome in tissues. 2025/09/03. Nature. DOI: https://doi.org/10.1038/s41586-025-09478-x.
Abstract
The spatial resolution of omics analyses is fundamental to understanding tissue biology1,2,3. The capacity to spatially profile DNA methylation, which is a canonical epigenetic mark extensively implicated in transcriptional regulation4,5, is lacking. Here we introduce a method for whole-genome spatial co-profiling of DNA methylation and the transcriptome of the same tissue section at near single-cell resolution. Applying this technology to mouse embryogenesis and the postnatal mouse brain resulted in rich DNA–RNA bimodal tissue maps. These maps revealed the spatial context of known methylation biology and its interplay with gene expression. The concordance and distinction in spatial patterns of the two modalities highlighted a synergistic molecular definition of cell identity in spatial programming of mammalian development and brain function. By integrating spatial maps of mouse embryos at two different developmental stages, we reconstructed the dynamics that underlie mammalian embryogenesis for both the epigenome and transcriptome, revealing details of sequence-, cell-type- and region-specific methylation-mediated transcriptional regulation. This method extends the scope of spatial omics to include DNA cytosine methylation, enabling a more comprehensive understanding of tissue biology across development and disease.
M. Angela Aznar, Charly R. Good, Julie S. Barber-Rotenberg, Sangya Agarwal, Wesley Wilson, Alex Watts, Zhen Zhang, Donna Gonzales, Greg Donahue, Wei-Ting Hwang, Austin K. Rennels, Andrew J. Rech, Shunichiro Kuramitsu, Hua Huang, Karl M. Glastad, Katherine A. Alexander, Gabriela Plesa, Emily Dowd, Andrea Brennan, Donald L. Siegel, Janos Tanyi, Andrew Haas, Drew A. Torigian, Gregory Nadolski, Vanessa E. Gonzalez, Elizabeth O. Hexner, Joseph A. Fraietta, Julie K. Jadlowsky, Regina M. Young, Shelley L. Berger, Carl H. June, Mark H. O’Hara. Clinical and molecular dissection of CAR T cell resistance in pancreatic cancer. Cell Reports Medicine. 2025/08/25. DOI: https://doi.org/10.1016/j.xcrm.2025.102301.
Summary
Patients with advanced pancreatic ductal adenocarcinoma (PDAC) have a median survival of less than a year, highlighting the urgent need for treatment advancements. We report on a phase 1 clinical trial assessing the safety and feasibility of intravenous and local administration of anti-mesothelin CAR T cells in patients with advanced PDAC. While therapy is well tolerated, it demonstrates limited clinical efficacy. Analyses of patient samples provide insights into mechanisms of treatment resistance. Single-cell genomic approaches reveal that post-infusion CAR T cells express exhaustion signatures, including previously identified transcription factors ID3 and SOX4, and display enrichment for a GZMK+ phenotype. Single knockout of ID3 or SOX4 enhances efficacy in xenograft models, though with donor-dependent variability. However, single-knockout cells eventually fail. Conversely, ID3 and SOX4 double-knockout CAR T cells exhibit prolonged relapse-free survival, demonstrating a sustained therapeutic effect and a potential avenue for engineering more potent CAR T cells in PDAC. This study was registered at ClinicalTrials.gov (NCT03323944).
Michelangelo B. Gonzatti, Jordi C.J. Hintzen, Isha Sharma, Mohd.Altaf Najar, Takeshi Tsusaka, Mariola M. Marcinkiewicz, Claudia Veronica Da Silva Cirspim, Nathaniel W. Snyder, George M. Burslem, Emily L. Goldberg. Class I histone deacetylases catalyze lysine lactylation. Journal of Biological Chemistry, 2025/08.25. DOI: 10.1016/j.jbc.2025.110602. https://doi.org/10.1016/j.jbc.2025.110602.
Abstract
Metabolism and post-translational modifications (PTMs) are intrinsically linked and the number of identified metabolites that can covalently modify proteins continues to increase. This metabolism/PTM crosstalk is especially true for lactate, the product of anaerobic metabolism following glycolysis. Lactate forms an amide bond with the ε-amino group of lysine, a modification known as lysine lactylation, or Kla. Multiple independent mechanisms have been proposed in the formation of Kla, including p300/CBP-dependent transfer from lactyl-CoA, a reactive intermediate lactoylglutathione species that non-enzymatically lactylates proteins, and several enzymes are reported to have lactyl transferase capability. We recently discovered that class I histone deacetylases (HDACs) 1, 2, and 3 can all reverse their canonical chemical reaction to catalyze lysine β-hydroxybutyrylation. Here we tested the hypothesis that HDACs can also catalyze Kla formation. Using biochemical, pharmacological, and genetic approaches, we found that HDACs are sufficient to catalyze Kla formation and that HDACs are a major driver of lysine lactylation. Dialysis experiments confirm this is a reversible reaction that depends on lactate concentration. We also directly quantified intracellular lactyl-CoA and found that Kla abundance can be uncoupled from lactyl-CoA levels. Therefore, we propose a model in which the majority of Kla is formed through enzymatic addition of lactate by HDACs 1, 2, and 3.
Kehui Zhu, Jinchao Chen, Long Zhao, Fangfang Lu, Jia Deng, Xuelei Lin, Chongsheng He, Doris Wagner, Jun Xiao. Dynamic control of H2A.Zub and H3K27me3 by ambient temperature during cell fate determination in Arabidopsis. Dev Cell. 2025 Aug 18;60(16):2192-2208.e5. doi: 10.1016/j.devcel.2025.04.002. Epub 2025 Apr 22. PMID: 40267908.
Abstract
Crucial to plant development, ambient temperature triggers intricate mechanisms enabling adaptive responses to temperature variations. The precise coordination of chromatin modifications in shaping cell developmental fate under diverse temperatures remains elusive. Our study, integrating comprehensive transcriptome, epigenome profiling, and genetics, demonstrates that lower ambient temperature (16°C) partially restores developmental defects caused by H3K27me3 loss in prc2 mutants by specifically depositing H2A.Zub at ectopically expressed embryonic genes in Arabidopsis, such as ABA INSENSITIVE 3 (ABI3) and LEAFY COTYLEDON 1 (LEC1). This deposition leads to downregulation of these genes and compensates for H3K27me3 depletion. Polycomb-repressive complex 1 (PRC1)-catalyzed H2A.Zub and PRC2-catalyzed H3K27me3 play roles in silencing transcription of embryonic genes for post-germination development. Low-temperature-induced reduction of TOE1 protein level decelerates H2A.Z turnover at specific loci, sustaining repression of embryonic genes and alleviating requirement for PRC2-H3K27me3 at post-germination stage. Our findings offer mechanistic insights into the cooperative epigenetic layers, facilitating plant adaptation to varying environmental temperatures.
Pu Zhang, Zhendong Cao, Xiangyu Pan, Yuqiao Liu, Cynthia Castro, Won Jun Kim, Takeshi Fujino, Jennifer Lewis, Jahan Rahman, Sanam Shahid, Jasmine Um, Erin Burns, Bingyi Chen, Winson Cai, Juliana Ortiz-Pacheco, Zhuoning Li, Mara Monetti, Christopher R. Vakoc, Anthony F. Daniyan, Omar Abdel-Wahab, Junwei Shi. Systematic evaluation of GAPs and GEFs identifies a targetable dependency for hematopoietic malignancies, Cancer Discovery, 2025. https://doi.org/10.1158/2159-8290.CD-25-0299.
Abstract
GAPs (GTPase-activating proteins) and GEFs (guanine nucleotide exchange factors) play key roles in cancer development, but their large number and potential redundancy have limited systematic evaluation. Here we perform unbiased genetic screens to identify GAPs and GEFs with cancer- and lineage-specific requirements, as well as dual perturbation screens to dissect functionally relevant interactors of GAPs and GEFs. Application to primary acute myeloid leukemia (AML) patient specimens uncovers the GAP ARHGAP45 as a targetable dependency shared across cancers of hematopoietic origin while being dispensable in normal hematopoiesis. We demonstrate that targeting ARHGAP45-expressing cells can be achieved through TCR-CAR T cells directed at an ARHGAP45-encoded minor histocompatibility antigen and that pharmacologic targeting of GAPs required upon ARHGAP45 depletion augments ARHGAP45-directed cell therapies. These studies provide a resource for probing oncogenic and druggable regulators of GTPases and strategies to target a GAP that represents a shared dependency across blood cancers.
Parisa Samareh, Paula Agudelo-Garcia, Zhen Zhang, Michael Gilbert, Mariel Mendoza, Hua Huang, Jennifer E Wu, Amy E Baxter, Zeyu Chen, Kate Alexander, E John Wherry, Charly R Good, Shelley L Berger, Chromatin repression by PRC2 results in reduced gene expression driving key features of CD8 T cell exhaustion, The Journal of Immunology, 2025;, vkaf188, https://doi.org/10.1093/jimmun/vkaf188
Abstract
Exhausted CD8 T cells result from chronic antigen stimulation and have reduced ability to clear disease. The epigenetic regulation of the dysfunctional phenotype of exhausted CD8 T cells is a promising avenue for therapies aimed at reversing or preventing CD8 T cell exhaustion. Here, utilizing in vitro and in vivo models, we show global increase of the repressive histone modification H3K27me3 in CD8 T cell exhaustion and increased gene expression of the EZH2 form of the PRC2 complex, which is responsible for H3K27me3 deposition. H3K27me3 correlated with decreased gene expression and localized to naive/memory T cell genes in CD8 T cell exhaustion. PRC2 inhibition increased expression of the naive/memory genes while reducing expression of key exhaustion genes. Further, we identified potential enhancers and transcription factors predicted to promote expression of the PRC2 subunits. Our study highlights the importance of the repressive epigenetic landscape of exhausted CD8 T cells as well as a novel role for PRC2 in T cell biology.
Logsdon, G.A., Ebert, P., Audano, P.A. et al. Complex genetic variation in nearly complete human genomes. Nature (2025). https: //doi.org/10.1038/s41586-025-09140-6
Abstract
Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (median continuity of 130 Mb), closing 92% of all previous assembly gaps and reaching telomere-to-telomere status for 39% of the chromosomes. We highlight complete sequence continuity of complex loci, including the major histocompatibility complex (MHC), SMN1/SMN2, NBPF8 and AMY1/AMY2, and fully resolve 1,852 complex structural variants. In addition, we completely assemble and validate 1,246 human centromeres. We find up to 30-fold variation in α-satellite higher-order repeat array length and characterize the pattern of mobile element insertions into α-satellite higher-order repeat arrays. Although most centromeres predict a single site of kinetochore attachment, epigenetic analysis suggests the presence of two hypomethylated regions for 7% of centromeres. Combining our data with the draft pangenome reference1 significantly enhances genotyping accuracy from short-read data, enabling whole-genome inference to a median quality value of 45. Using this approach, 26,115 structural variants per individual are detected, substantially increasing the number of structural variants now amenable to downstream disease association studies.
Aishwarya S. Pawar, Patrick Somers, Aleena Alex, Jason Grana, Victoria K. Feist, Subin S. George, Sapana S. Jalnapurkar, Charles Antony, Roman Verner, Sanese K. White-Brown, Mohit Khera, María Saraí Mendoza-Figueroa, Kathy Fange Liu, Jennifer J.D. Morrissette, Sandeep Gurbuxani, & Vikram R. Paralkar. Leukemia mutated proteins PHF6 and PHIP form a chromatin complex that represses acute myeloid leukemia stemness. Genes & Dev, 2025. DOI: 10.1101/gad.352602.125.
Abstract
Myeloid leukemias are heterogeneous cancers with diverse mutations, sometimes in genes with unclear roles and unknown functional partners. PHF6 and PHIP are two poorly understood chromatin-binding proteins recurrently mutated in acute myeloid leukemia (AML). PHF6 mutations are associated with poorer outcomes, whereas PHIP was recently identified as the most common selective mutation in Black patients with AML. Here, we show that Phf6 knockout converts Flt3-ITD-driven mouse chronic myelomonocytic leukemia (CMML) into AML with reduced survival. Using cell line models, we show that PHF6 is a transcriptional repressor that suppresses a limited stemness gene network and that PHF6 missense mutations, classified by current clinical algorithms as variants of unknown significance, produce unstable or nonfunctional protein. We present multiple lines of evidence converging on a critical mechanistic connection between PHF6 and PHIP. We show that PHIP loss phenocopies PHF6 loss and that PHF6 requires PHIP to occupy chromatin and exert its downstream transcriptional program. Our work unifies PHF6 and PHIP, two disparate leukemia mutated proteins, into a common functional complex that suppresses AML stemness.
Randi Isenhart, Son C. Nguyen, Leah Rosin, Weihuan Cao, Patrick Walsh, Haris Muzaffar, Christopher E. Ellison, and Eric F. Joyce. The length and strength of compartmental interactions are modulated by condensin II activity. PLOS Genetics, July 1, 2025. https://doi.org/10.1371/journal.pgen.1011724
Abstract
The spatial organization of the genome is crucial for its function and integrity. Although the ring-like SMC complex condensin II has a well-documented role in organizing mitotic chromosomes, its function in interphase chromatin structure has remained more enigmatic. Using a combination of Oligopaint fluorescence in situ hybridization (FISH) and Hi-C, we show that altering condensin II levels in diploid Drosophila cells significantly changes chromosome architecture at large length scales between chromatin compartments. Notably, condensin II overexpression disrupts the robust boundary between heterochromatin and euchromatin, leading to interactions that span entire chromosomes. These interactions occur independent from transcriptional changes, suggesting that the mechanisms driving compartment formation and their interactions might be distinct aspects of genome organization. Our results provide new insights into the dynamic nature of chromosome organization and underscore the importance of condensin II in maintaining genomic stability.
Pengfei Guo, Yufan Chen, Liran Mao, Angelysia Cardilla, Chin Nien Lee, Yan Cui, Dengge Jin, Yucong Hua, Xiaowei Xu & Yanxiang Deng. Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues. Nat Commun 16, 5945 (2025). https://doi.org/10.1038/s41467-025-60882-3.
Abstract
Formalin-fixed paraffin-embedded (FFPE) samples represent a vast, untapped resource for epigenomic research, yet molecular tools for deep analysis of these specimens remain limited. We introduce spatial FFPE-ATAC-seq, an approach for in situ profiling chromatin accessibility within archived tissues. This approach overcomes formalin-induced crosslinking challenges, allowing high-resolution mapping of chromatin landscapes while preserving tissue architecture. Applying spatial FFPE-ATAC-seq to mouse and human tissues, including brain and thymus, reveals intricate spatial organization and distinct cell types in alignment with tissue morphology. Integration with single-cell RNA sequencing validates the precision of our chromatin profiles in identifying key cell types and regulatory elements. We further apply this method to human melanoma, comprehensively characterizing chromatin accessibility across both tumor and non-tumor regions. This method significantly expands the toolkit for epigenomic research, unlocking the potential of an extensive collection of archived FFPE samples for studying gene regulation and disease mechanisms with spatial context.
Marissa J Maroni, Melissa Barton, Katherine Lynch, Ashish R Deshwar, Philip D Campbell, Josephine Millard, Rachel Lee, Annastelle Cohen, Rili Ahmad, Alekh Paranjapye, Víctor Faundes, Gabriela M Repetto, Caoimhe McKenna, Amelle L Shillington, Chanika Phornphutkul, Hanne B Hove, Grazia M S Mancini, Rachel Schot, Tahsin Stefan Barakat, Christopher M Richmond, Julie Lauzon, Ahmed Ibrahim Elsayed Ibrahim, Caroline Nava, Delphine Héron, Minke M A van Aalst, Slavena Atemin, Mila Sleptsova, Iliyana Aleksandrova, Albena Todorova, Debra L Watkins, Mariya A Kozenko, Daniel Natera-de Benito, Carlos Ortez, Berta Estevez-Arias, François Lecoquierre, Kévin Cassinari, Anne-Marie Guerrot, Jonathan Levy, Xenia Latypova, Alain Verloes, A Micheil Innes, Xiao-Ru Yang, Siddharth Banka, Katharina Vill, Maureen Jacob, Michael Kruer, Peter Skidmore, Carolina I Galaz-Montoya, Somayeh Bakhtiari, Jessica L Mester, Michael Granato, Karim-Jean Armache, Gregory Costain, Erica Korb. Loss of DOT1L disrupts neuronal transcription and leads to a neurodevelopmental disorder. Brain. 2025 Jun 11:awaf212. doi: 10.1093/brain/awaf212. PMID: 40494548.
Abstract
Individuals with monoallelic gain-of-function variants in the histone lysine methyltransferase DOT1L display global developmental delay and varying congenital anomalies. However, the impact of monoallelic loss of DOT1L remains unclear. Here, we sought to define the effects of partial DOT1L loss by applying bulk and single-nucleus RNA-sequencing, ChIP-sequencing, imaging, multielectrode array recordings, and behavioral analysis of zebrafish and multiple mouse models. We present a cohort of 16 individuals (12 females, 4 males) with neurodevelopmental disorders and monoallelic DOT1L variants, including a frameshift deletion, an in-frame deletion, a nonsense, and missense variants clustered in the catalytic domain. We demonstrate that specific variants cause loss of methyltransferase activity. In primary cortical neurons, Dot1l knockdown disrupts transcription of synaptic genes, neuron branching, expression of a synaptic protein, and neuronal activity. Further in the cortex of heterozygous Dot1l mice, Dot1l loss causes sex-specific transcriptional responses and H3K79me2 depletion, including within down-regulated genes. Lastly using both zebrafish and mouse models, we found behavioral disruptions that include developmental deficits and sex-specific social behavioral changes. Overall, we define how DOT1L loss leads to neurological dysfunction by demonstrating that partial Dot1l loss impacts neuronal transcription, neuron morphology, and behavior across multiple models and systems.
Michael B Gilbert, Karl M Glastad, Maxxum Fioriti, Matan Sorek, Tierney Scarpa, Freddy S Purnell, Daniel Xu, Lindsay K Pino, Anatoly Korotkov, Ali Biashad, Josue Baeza, Richard Lauman, Anastasiia Filippova, Balint Z Kacsoh, Roberto Bonasio, Mackenzie W Mathis, Benjamin A Garcia, Andrei Seluanov, Vera Gorbunova, Shelley L Berger. Neuropeptides specify and reprogram division of labor in the leafcutter ant Atta cephalotes. Cell. 2025 Jun 9:S0092-8674(25)00573-2. doi: 10.1016/j.cell.2025.05.023. PMID: 40505655.
Abstract
Social insects offer powerful models to investigate mechanisms of elaborate individual behaviors comprising a cooperative community. Workers of the leafcutter ant genus Atta are extreme examples of behavioral segregation among phenotypically distinct worker types. We utilize this worker system to test the molecular underpinnings of behavioral programming and the extent of plasticity to reprogramming. We identify specific neuropeptides mediating worker division of labor in A. cephalotes, finding two neuropeptides associated with characteristic behaviors of leaf cutting and of brood care. Genetic knockdown or injection of these neuropeptides led to a stark gain or loss of each behavior and to transcriptomic shifts toward gene pathways expressed in the natural castes. We also reveal global similarities between worker transcriptomes of the eusocial mammal, the naked mole-rat H. glaber, with orthologous A. cephalotes workers. This work underscores the essential function of neuropeptides in establishing complex social behavior and a remarkable plasticity among individual behavioral types.
Khoa A. Tran, Michael Gilbert, Berta N. Vazquez, Alessandro Ianni, Benjamin A. Garcia, Alejandro Vaquero, Shelley L. Berger. SIRT7 regulates NUCKS1 chromatin binding to elicit metabolic and inflammatory gene expression in senescence and liver aging. Molecular Cell, 2025, ISSN 1097-2765, https://doi.org/10.1016/j.molcel.2025.05.025.
Gina N. Pacella, Nina Kupraserkul, Lydia Bao, Sijia Huang, Carina D’souza, Stephen M. Prouty, Amy Anderson, Alexandra M. Maldonado López, Morgan Sinkfield, Cyria Olingou, John T. Seykora, & Brian C. Capell. UTX (KDM6A) promotes differentiation noncatalytically in somatic self-renewing epithelia, Proc. Natl. Acad. Sci. U.S.A. 122 (20) e2422971122, https://doi.org/10.1073/pnas.2422971122 (2025).
Abstract
Jenna N Beyer, Yevgeniy V Serebrenik, Kaitlyn Toy, Mohd Altaf Najar, Emily Feierman, Nicole R Raniszewski, Erica Korb, Ophir Shalem, George M Burslem. Intracellular protein editing enables incorporation of noncanonical residues in endogenous proteins. Science. 2025 May;388(6746):eadr5499. doi: 10.1126/science.adr5499. Epub 2025 May 1. PMID: 40310911.
Abstract
The ability to study proteins in their native cellular context is crucial to our understanding of biology. In this work, we report a technology for intracellular protein editing, drawing from split intein-mediated protein splicing, genetic code expansion, and endogenous protein tagging. This approach enables us to rapidly and site-specifically install residues and chemical handles into a protein. We demonstrate the power of this platform to edit cellular proteins, inserting epitopes, protein-specific sequences, and noncanonical amino acids. Notably, we use an endogenous tagging approach to apply our protein editing technology to endogenous proteins with minimal perturbation. We anticipate that the protein editing technology presented in this work will be applied to a diverse set of problems and phenomena in live mammalian cells.
Julianna G. Supplee, Ronen Marmorstein, Kathryn E. Wellen. Molecular targets of bempedoic acid and related decoy fatty acids. Trends in Endocrinology & Metabolism. DOI: 10.1016/j.tem.2025.04.002.
Abstract
Disorders of lipid metabolism, including hyperlipidemia, atherosclerosis, and metabolic dysfunction-associated steatotic liver disease, are increasing across the globe. Bempedoic acid (BPA) is a first-in-class drug for the treatment of hypercholesterolemia and cardiac risk reduction, which may particularly benefit those who do not tolerate statins. Inhibition of hepatic ATP-citrate lyase (ACLY) is widely accepted as the main mediator of its observed clinical effects. However, BPA treatment also has ACLY-independent effects on lipid metabolism, as the structural similarity of BPA to endogenous fatty acids allows it to trigger multiple lipid-signaling pathways. Here, we review the molecular targets of BPA and related ‘decoy fatty acid’ drugs and identify areas where further study is warranted as these molecules are evaluated for clinical indications.
Keegan S Krick, Marissa Maroni, Erica Korb, Kristen Lynch, and Elizabeth Heller. Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing. Genome Res, 2025. DOI: 10.1101/gr.280082.124
Abstract
Activity-dependent gene expression in neurons is well-established, yet few studies have examined activity-dependent alternative splicing. Alternative splicing regulates >95% of genes and is essential to diverse neuronal functions, including synapse development and calcium channel diversity. Alternative splicing is regulated by the expression and activity of RNA-binding proteins and through changes in the local chromatin environment. To date, most analyses of activity-dependent alternative splicing are focus primarily on microexons, a small subclass of neuron-specific exons. To broaden knowledge of activity-dependent alternative splicing in neurons, we analyzed five independent RNA-seq studies to identify splicing events that consistently respond to potassium chloride (KCl) depolarization. We found that the majority of activity-dependent exons become less included upon activation, are basally constitutive, are not microexons, and reside in genes that are not differentially expressed after KCl treatment. Functionally, alternative splicing of RNA processing machinery and regulators precedes splicing of genes related to neuronal function. Given recent advances in elucidating chromatin-mediated alternative splicing in brain, we explored the coincident regulation of histone modifications over activity-dependent exons. We found KCl-dependent changes in H3K36me3 and H4K20me1, both enriched in active gene bodies, over a subset of KCl-dependent exons, suggesting coordination of activity-dependent histone modification and alternative splicing. Together, these findings identify a diverse class of activity-dependent alternative splicing and describes the temporality and features of its regulation in cultured neurons.
Marcus Woodworth, Tristan Mcdonnell, and Melike Lakadamyali. BPS2025 – Visualizing chromatin states in native contexts using expansion microscopy. Biophysical Journal (2025). DOI: https://doi.org/10.1016/j.bpj.2024.11.080.
Abstract
The nanoscale arrangement of chromatin within the nuclei of cells has been implicated in the establishment of cell identity during development and disease progression. As such, much research has been dedicated to studying this architecture in bulk cell studies, where state heterogeneity is lost, or in isolated cells that are devoid of their tissue context features. This is because there are few strategies available to visualizing nanoscale chromatin architecture within the native tissue, particularly those with dense extracellular matrices (ECMs), or at length scales relevant to gene activation. For example, although we have demonstrated that the chromatin organization of isolated tendon cells depend on surface stiffness, and isolated tendon cells from tendinosis patient show remarkable changes in nanoscale chromatin organization compared to cells from healthy patients, we have yet to see how each cells micro-environment relates to their chromatin state. To address this need, we have adapted the novel method fluorescent labeling of abundant reactive entities (FLARE) along with expansion microscopy (ExM) to visualize chromatin features of cells within their native and dense ECM environment. FLARE provides details of both ECM matrix uniformity and composition for multiple tissue types and species (e.g., mouse and bovine tendons). We also show our method is compatible with histone mark staining and capable of revealing relationships between ECM matrix heterogeneity and chromatin state distributions for multiple cell types. We anticipate the application of these novel methods will uncover the epigenetic changes in healthy and diseased cells within tissue, such as for tendinopathy progression, while creating the possibility for future therapeutics that target epigenetic states for better patient outcomes in multiple tissue modalities.
Kollin Schultz, Pedro Costa-Pinheiro, Lauren Gardner, Laura V. Pinheiro, Julio Ramirez-Solis, Sarah M. Gardner, Kathryn E. Wellen, and Ronen Marmorstein. Snapshots of acyl carrier protein shuttling in human fatty acid synthase. Nature (2025). https://doi.org/10.1038/s41586-025-08587-x
Abstract
The mammalian fatty acid synthase (FASN) enzyme is a dynamic multienzyme that belongs to the megasynthase family. In mammals, a single gene encodes six catalytically active domains and a flexibly tethered acyl carrier protein (ACP) domain that shuttles intermediates between active sites for fatty acid biosynthesis1. FASN is an essential enzyme in mammalian development through the role that fatty acids have in membrane formation, energy storage, cell signalling and protein modifications. Thus, FASN is a promising target for treatment of a large variety of diseases including cancer, metabolic dysfunction-associated fatty liver disease, and viral and parasite infections2,3. The multi-faceted mechanism of FASN and the dynamic nature of the protein, in particular of the ACP, have made it challenging to understand at the molecular level. Here we report cryo-electron microscopy structures of human FASN in a multitude of conformational states with NADPH and NADP+ plus acetoacetyl-CoA present, including structures with the ACP stalled at the dehydratase (DH) and enoyl-reductase (ER) domains. We show that FASN activity in vitro and de novo lipogenesis in cells is inhibited by mutations at the ACP–DH and ACP–ER interfaces. Together, these studies provide new molecular insights into the dynamic nature of FASN and the ACP shuttling mechanism, with implications for developing improved FASN-targeted therapeutics.
Ruofan Yu, Shelby Roseman, Allison P. Siegenfeld, Zachary Gardner, Son C. Nguyen, Khoa A. Tran, Eric F. Joyce, Rajan Jain, Brian B. Liau, Ian D. Krantz, Katherine A. Alexander & Shelley L. Berger. CTCF/RAD21 organize the ground state of chromatin–nuclear speckle association. Nat Struct Mol Biol (2025). https://doi.org/10.1038/s41594-024-01465-6
Abstract
Recent findings indicate that nuclear speckles, a distinct type of nuclear body, interact with certain chromatin regions in a ground state. Here, we report that the chromatin structural factors CTCF and cohesin are required for full ground-state association between DNA and nuclear speckles. We identified a putative speckle-targeting motif (STM) within cohesin subunit RAD21 and demonstrated that the STM is required for chromatin–nuclear speckle association, disruption of which also impaired induction of speckle-associated genes. Depletion of the cohesin-releasing factor WAPL, which stabilizes cohesin on chromatin, resulted in reinforcement of DNA–speckle contacts and enhanced inducibility of speckle-associated genes. Additionally, we observed disruption of chromatin–nuclear speckle association in patient-derived cells with Cornelia de Lange syndrome, a congenital neurodevelopmental disorder involving defective cohesin pathways. In summary, our findings reveal a mechanism for establishing the ground state of chromatin–speckle association and promoting gene inducibility, with relevance to human disease.
Emily S. Smith-Pillet, Ramya Billur, Marie-France Langelier, Tanaji T. Talele, John M. Pascal, Ben E. Black. A PARP2 active site helix melts to permit DNA damage-induced enzymatic activation. Molecular Cell. DOI: https://doi.org/10.1016/j.molcel.2025.01.004
Summary
Poly(ADP-ribose) polymerase 1 (PARP1) and PARP2 recognize DNA breaks immediately upon their formation, generate a burst of local PARylation to signal their location, and are co-targeted by all current FDA-approved forms of PARP inhibitors (PARPi) used in the cancer clinic. Recent evidence indicates that the same PARPi molecules impact PARP2 differently from PARP1, raising the possibility that allosteric activation may also differ. We find that, unlike for PARP1, destabilization of the autoinhibitory domain of PARP2 is insufficient for DNA damage-induced catalytic activation. Rather, PARP2 activation requires further unfolding of an active site helix. In contrast, the corresponding helix in PARP1 only transiently forms, even prior to engaging DNA. Only one clinical PARPi, Olaparib, stabilizes the PARP2 active site helix, representing a structural feature with the potential to discriminate small molecule inhibitors. Collectively, our findings reveal unanticipated differences in local structure and changes in activation-coupled backbone dynamics between human PARP1 and PARP2.
Pengfei Guo, Liran Mao, Yufan Chen, Chin Nien Lee, Angelysia Cardilla, Mingyao Li, Marek Bartosovic, Yanxiang Deng. Multiplexed spatial mapping of chromatin features, transcriptome and proteins in tissues. Nat Methods (2025). https://doi.org/10.1038/s41592-024-02576-0
Abstract
The phenotypic and functional states of cells are modulated by a complex interactive molecular hierarchy of multiple omics layers, involving the genome, epigenome, transcriptome, proteome and metabolome. Spatial omics approaches have enabled the study of these layers in tissue context but are often limited to one or two modalities, offering an incomplete view of cellular identity. Here we present spatial-Mux-seq, a multimodal spatial technology that allows simultaneous profiling of five different modalities: two histone modifications, chromatin accessibility, whole transcriptome and a panel of proteins at tissue scale and cellular level in a spatially resolved manner. We applied this technology to mouse embryos and mouse brains, generating detailed multimodal tissue maps that identified more cell types and states compared to unimodal data. This analysis uncovered spatiotemporal relationships among histone modifications, chromatin accessibility, gene expression and protein levels during neuron differentiation, and revealed a radial glia niche with spatially dynamic epigenetic signals. Collectively, the spatial multi-omics approach heralds a new era for characterizing tissue and cellular heterogeneity that single-modality studies alone could not reveal.
Nicholas G. Aboreden, Jessica C. Lam, Viraat Y. Goel, Siqing Wang, Xiaokang Wang, Susannah C. Midla, Alma Quijano, Cheryl A. Keller, Belinda M. Giardine, Ross C. Hardison, Haoyue Zhang, Anders S. Hansen, Gerd A. Blobel. LDB1 establishes multi-enhancer networks to regulate gene expression. Molecular Cell, Volume 85, Issue 2, 2025, Pages 376-393.e9. ISSN 1097-2765. DOI: https://doi.org/10.1016/j.molcel.2024.11.037
Summary
Katherine A. Alexander, Ruofan Yu, Nicolas Skuli, Nathan J. Coffey, Son Nguyen, Christine L. Faunce, Hua Huang, Ian P. Dardani, Austin L. Good, Joan Lim, Catherine Y. Li, Nicholas Biddle, Eric F. Joyce, Arjun Raj, Daniel Lee, Brian Keith, M. Celeste Simon, & Shelley L. Berger. Nuclear speckles regulate functional programs in cancer. Nat Cell Biol (2025). https://doi.org/10.1038/s41556-024-01570-0
Abstract
Nuclear speckles are dynamic nuclear bodies characterized by high concentrations of factors involved in RNA production. Although the contents of speckles suggest multifaceted roles in gene regulation, their biological functions are unclear. Here we investigate speckle variation in human cancer, finding two main signatures. One speckle signature was similar to healthy adjacent tissues, whereas the other was dissimilar, and considered an aberrant cancer speckle state. Aberrant speckles show altered positioning within the nucleus, higher levels of the TREX RNA export complex and correlate with poorer patient outcomes in clear cell renal cell carcinoma (ccRCC), a cancer typified by hyperactivation of the HIF-2α transcription factor. We demonstrate that HIF-2α promotes physical association of certain target genes with speckles depending on HIF-2α protein speckle-targeting motifs, defined in this study. We identify homologous speckle-targeting motifs within many transcription factors, suggesting that DNA-speckle targeting may be a general gene regulatory mechanism. Integrating functional, genomic and imaging studies, we show that HIF-2α gene regulatory programs are impacted by speckle state and by abrogation of HIF-2α-driven speckle targeting. These findings suggest that, in ccRCC, a key biological function of nuclear speckles is to modulate expression of select HIF-2α-regulated target genes that, in turn, influence patient outcomes. Beyond ccRCC, tumour speckle states broadly correlate with altered functional pathways and expression of speckle-associated gene neighbourhoods, exposing a general link between nuclear speckles and gene expression dysregulation in human cancer.
Damian Dudka, Jennine M. Dawicki-McKenna, Xueqi Sun, Keagan Beeravolu, Taksahi Akera, Michael A. Lampson, & Ben E. Black. Satellite DNA shapes dictate pericentromere packaging in female meiosis. Nature (2025). https://doi.org/10.1038/s41586-024-08374-0
Abstract
The abundance and sequence of satellite DNA at and around centromeres is evolving rapidly despite the highly conserved and essential process through which the centromere directs chromosome inheritance. The impact of such rapid evolution is unclear. Here we find that sequence-dependent DNA shape dictates packaging of pericentromeric satellites in female meiosis through a conserved DNA-shape-recognizing chromatin architectural protein, high mobility group AT-hook 1 (HMGA1). Pericentromeric heterochromatin in two closely related mouse species, M. musculus and M. spretus, forms on divergent satellites that differ by both density of narrow DNA minor grooves and HMGA1 recruitment. HMGA1 binds preferentially to M. musculus satellites, and depletion in M. musculus oocytes causes massive stretching of pericentromeric satellites, disruption of kinetochore organization and delays in bipolar spindle assembly. In M. musculus × spretus hybrid oocytes, HMGA1 depletion disproportionately impairs M. musculus pericentromeres and microtubule attachment to their kinetochores. Thus, DNA shape affects both pericentromere packaging and the segregation machinery. We propose that rapid evolution of centromere and pericentromere DNA does not disrupt these essential processes when the satellites adopt DNA shapes recognized by conserved architectural proteins (such as HMGA1). By packaging these satellites, architectural proteins become part of the centromeric and pericentromeric chromatin, suggesting an evolutionary strategy that lowers the cost of megabase-scale satellite expansion.
Varun Bahl, Reut Rifkind, Eric Waite, Zenab Hamdan, Catherine Lee May, Elisabetta Manduchi, Benjamin F. Voight, Michelle Y.Y. Lee, Mark Tigue, Nicholas Manuto, Benjamin Glaser, Dana Avrahami, Klaus H. Kaestner. G6PC2 controls glucagon secretion by defining the set point for glucose in pancreatic α cells. Science Translational Medicine (2025). DOI: https://doi.org/10.1126/scitranslmed.adi6148.
Abstract
Jailynn Harke, Jeewon R. Lee, Son C. Nguyen, Arian Arab, Staci M. Rakowiecki, Siewert Hugelier, Christina Paliou, Antonella Rauseo, Rebecca Yunker, Kellen Xu, Yao Yao, Melike Lakadamyali, Guillaume Andrey, Douglas J. Epstein, Eric F. Joyce. Multiple allelic configurations govern long-range Shh enhancer-promoter communication in the embryonic forebrain. Molecular Cell. DOI: https://doi.org/10.1016/j.molcel.2024.10.042.
Summary
Developmental gene regulation requires input from enhancers spread over large genomic distances. Our understanding of long-range enhancer-promoter (E-P) communication, characterized as loops, remains incomplete without addressing the role of intervening chromatin. Here, we examine the topology of the entire Sonic hedgehog (Shh) regulatory domain in individual alleles from the mouse embryonic forebrain. Through sequential Oligopaint labeling and super-resolution microscopy, we find that the Shh locus maintains a compact structure that adopts several diverse configurations independent of Shh expression. The most frequent configuration contained distal E-P contacts at the expense of those more proximal to Shh, consistent with an interconnected loop. Genetic perturbations demonstrate that this long-range E-P communication operates by Shh-expression-independent and dependent mechanisms, involving CTCF binding sites and active enhancers, respectively. We propose a model whereby gene regulatory elements secure long-range E-P interactions amid an inherent architectural framework to coordinate spatiotemporal patterns of gene expression.
Ashton S. Holub, Sarah G. Choudury, Ekaterina P. Andrianova, Courtney E. Dresden, Ricardo Urquidi Camacho, Igor B. Zhulin, Aman Y. Husbands. START domains generate paralog-specific regulons from a single network architecture. Nat Commun 15, 9861 (2024). https://doi.org/10.1038/s41467-024-54269-z
Abstract
Functional divergence of transcription factors (TFs) has driven cellular and organismal complexity throughout evolution, but its mechanistic drivers remain poorly understood. Here we test for new mechanisms using CORONA (CNA) and PHABULOSA (PHB), two functionally diverged paralogs in the CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) family of TFs. We show that virtually all genes bound by PHB ( ~ 99%) are also bound by CNA, ruling out occupation of distinct sets of genes as a mechanism of functional divergence. Further, genes bound and regulated by both paralogs are almost always regulated in the same direction, ruling out opposite regulation of shared targets as a mechanistic driver. Functional divergence of CNA and PHB instead results from differential usage of shared binding sites, with hundreds of uniquely regulated genes emerging from a commonly bound genetic network. Regulation of a given gene by CNA or PHB is thus a function of whether a bound site is considered ‘responsive’ versus ‘non-responsive’ by each paralog. Discrimination between responsive and non-responsive sites is controlled, at least in part, by their lipid binding START domain. This suggests a model in which HD-ZIPIII TFs use information integrated by their START domain to generate paralog-specific transcriptional outcomes from a shared network architecture. Taken together, our study identifies a mechanism of HD-ZIPIII TF paralog divergence and proposes the ubiquitously distributed START evolutionary module as a driver of functional divergence.
Jingchao Zhang, Greg Donahue, Michael B. Gilbert, Tomer Lapidot, Dario Nicetto, Kenneth S. Zaret. Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programmes and repeats in pluripotent cells. Nat Cell Biol (2024). https://doi.org/10.1038/s41556-024-01547-z
Abstract
H3K9me3 heterochromatin, established by lysine methyltransferases (KMTs) and compacted by heterochromatin protein 1 (HP1) isoforms, represses alternative lineage genes and DNA repeats. Our understanding of H3K9me3 heterochromatin stability is presently limited to individual domains and DNA repeats. Here we engineered Suv39h2-knockout mouse embryonic stem cells to degrade remaining two H3K9me3 KMTs within 1 hour and found that both passive dilution and active removal contribute to H3K9me3 decay within 12–24 hours. We discovered four different H3K9me3 decay rates across the genome and chromatin features and transcription factor binding patterns that predict the stability classes. A ‘binary switch’ governs heterochromatin compaction, with HP1 rapidly dissociating from heterochromatin upon KMT depletion and a particular threshold level of HP1 limiting pioneer factor binding, chromatin opening and exit from pluripotency within 12 h. Unexpectedly, receding H3K9me3 domains unearth residual HP1β peaks enriched with heterochromatin-inducing proteins. Our findings reveal distinct H3K9me3 heterochromatin maintenance dynamics governing gene networks and repeats that together safeguard pluripotency.
Sarah M. Gardner, Austin Vogt, Trevor M. Penning, Ronen Marmorstein. Substrate specificity and kinetic mechanism of 3-hydroxy-Δ5-C27-steroid oxidoreductase. Journal of Biological Chemistry. 2024. 107945, ISSN 0021-9258. DOI: https://doi.org/10.1016/j.jbc.2024.107945
Abstract
Cholesterol is a key sterol whose homeostasis is primarily maintained through bile acid metabolism. Proper bile acid formation is vital for nutrient and fat-soluble vitamin absorption and emulsification of lipids. Synthesis of bile acids occurs through two main pathways, both of which rely on 3-hydroxy-5-C27 steroid oxidoreductase (HSD3B7) to begin epimerization of the 3β hydroxyl of cholesterol into its active 3α conformation. In this sequence HSD3B7 catalyzes the dehydrogenation of the 3β-hydroxy group followed by isomerization of the Δ5-cholestene-3-one. These reactions are some of the many steps that transform cholesterol for either storage or secretion. HSD3B7 has distinct activity from other 3β-HSD family members leaving significant gaps in our understanding of its mode of catalysis and substrate specificity. Additionally, the role of HSD3B7 in health and disease positions it as a metabolic vulnerability that could be harnessed as a therapeutic target. To this end, we evaluated the mechanism of HSD3B7 catalysis and reveal that HSD3B7 displays activity towards diverse 7α-hydroxylated oxysterols. HSD3B7 retains its catalytic efficiency towards these substrates, suggesting that its substrate binding pocket can withstand changes in polarity upon alterations to this hydrocarbon tail. Experiments aimed at determining substrate order are consistent with HSD3B7 catalyzing a sequential ordered bi bi reaction mechanism with the binding of NAD+ followed by 7α-hydroxycholesterol to form a central complex. HSD3B7 bifunctional activity is dependent on membrane localization through a putative membrane-associated helix giving insight into potential regulation of enzyme activity. We found strong binding of the NADH product thought to activate the isomerization reaction. Homology models of HSD3B7 reveal a potential substrate pocket that allows for oxysterol binding and mutagenesis was utilized to support this model. Together these studies offer an understanding of substrate specificity and kinetic mechanism of HSD3B7 which can be exploited for future drug development.
Feng Zhang, Yao Fu, Dennissee Jimenez-Cyrus, Ting Zhao, Yachen Shen, Yusha Sun, Zhijian Zhang, Qing Wang, Riki Kawaguchi, Daniel H. Geschwind, Chuan He, Guo-li Ming, Hongjun Song. m6A/YTHDF2-mediated mRNA decay targets TGF-β signaling to suppress the quiescence acquisition of early postnatal mouse hippocampal NSCs. Cell Stem Cell. 2024. ISSN 1934-5909. DOI: https://doi.org/10.1016/j.stem.2024.10.002
Summary
Quiescence acquisition of proliferating neural stem cells (NSCs) is required to establish the adult NSC pool. The underlying molecular mechanisms are not well understood. Here, we showed that conditional deletion of the m6A reader Ythdf2, which promotes mRNA decay, in proliferating NSCs in the early postnatal mouse hippocampus elevated quiescence acquisition in a cell-autonomous fashion with decreased neurogenesis. Multimodal profiling of m6A modification, YTHDF2 binding, and mRNA decay in hippocampal NSCs identified shared targets in multiple transforming growth factor β (TGF-β)-signaling-pathway components, including TGF-β ligands, maturation factors, receptors, transcription regulators, and signaling regulators. Functionally, Ythdf2 deletion led to TGF-β-signaling activation in NSCs, suppression of which rescued elevated quiescence acquisition of proliferating hippocampal NSCs. Our study reveals the dynamic nature and critical roles of mRNA decay in establishing the quiescent adult hippocampal NSC pool and uncovers a distinct mode of epitranscriptomic control via co-regulation of multiple components of the same signaling pathway.
Joyce Y. Liu, Ramya S. Kuna, Laura V. Pinheiro, Phuong T.T. Nguyen, Jaclyn E. Welles, Jack M. Drummond, Nivitha Murali, Prateek V. Sharma, Julianna G. Supplee, Mia Shiue, Steven Zhao, Aimee T. Farria, Avi Kumar, Mauren L. Ruchhoeft, Christina Demetriadou, Daniel S. Kantner, Adam Chatoff, Emily Megill, Paul M. Titchenell, Nathaniel W. Snyder, Christian M. Metallo, & Kathryn E. Wellen. Bempedoic acid suppresses diet-induced hepatic steatosis independently of ATP-citrate lyase. Cell Metabolism. DOI: 10.1016/j.cmet.2024.10.014.
Summary
Charles Bond, Siewert Hugelier, Jiazheng Xing, Elena M. Sorokina, Melike Lakadamyali; Heterogeneity of late endosome/lysosomes shown by multiplexed DNA-PAINT imaging. J Cell Biol 6 January 2025; 224 (1): e202403116. doi: https://doi.org/10.1083/jcb.202403116
Abstract
Late endosomes/lysosomes (LELs) are crucial for numerous physiological processes and their dysfunction is linked to many diseases. Proteomic analyses have identified hundreds of LEL proteins; however, whether these proteins are uniformly present on each LEL, or if there are cell-type-dependent LEL subpopulations with unique protein compositions is unclear. We employed quantitative, multiplexed DNA-PAINT super-resolution imaging to examine the distribution of seven key LEL proteins (LAMP1, LAMP2, CD63, Cathepsin D, TMEM192, NPC1, and LAMTOR4). While LAMP1, LAMP2, and Cathepsin D were abundant across LELs, marking a common population, most analyzed proteins were associated with specific LEL subpopulations. Our multiplexed imaging approach identified up to eight different LEL subpopulations based on their unique membrane protein composition. Additionally, our analysis of the spatial relationships between these subpopulations and mitochondria revealed a cell-type-specific tendency for NPC1-positive LELs to be closely positioned to mitochondria. Our approach will be broadly applicable to determining organelle heterogeneity with single organelle resolution in many biological contexts.
Natalie A. Trigg, Colin C. Conine. Epididymal acquired sperm microRNAs modify post-fertilization embryonic gene expression. Cell Reports, Volume 43, Issue 9, 2024, 114698, ISSN 2211-1247, DOI: https://doi.org/10.1016/j.celrep.2024.114698.
Summary
Abstract
Jingru Zhao, Yeqiao Zhou, Illias Tzelepi, Noah G. Burget, Junwei Shi, & Robert B. Faryabi. Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells. 7 Aug 2024. Science Advances. DOI: 10.1126/sciadv.adl4043.
Abstract
Sequencing-based mapping of ensemble pairwise interactions among regulatory elements support the existence of topological assemblies known as promoter-enhancer hubs or cliques in cancer. Yet, prevalence, regulators, and functions of promoter-enhancer hubs in individual cancer cells remain unclear. Here, we systematically integrated functional genomics, transcription factor screening, and optical mapping of promoter-enhancer interactions to identify key promoter-enhancer hubs, examine heterogeneity of their assembly, determine their regulators, and elucidate their role in gene expression control in individual triple negative breast cancer (TNBC) cells. Optical mapping of individual SOX9 and MYC alleles revealed the existence of frequent multiway interactions among promoters and enhancers within spatial hubs. Our single-allele studies further demonstrated that lineage-determining SOX9 and signaling-dependent NOTCH1 transcription factors compact MYC and SOX9 hubs. Together, our findings suggest that promoter-enhancer hubs are dynamic and heterogeneous topological assemblies, which are controlled by oncogenic transcription factors and facilitate subtype-restricted gene expression in cancer.
Brent S. Perlman, Noah Burget, Yeqiao Zhou, Gregory W. Schwartz, Jelena Petrovic, Zora Modrusan & Robert B. Faryabi. Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance. Nat Commun 15, 8070 (2024). https://doi.org/10.1038/s41467-024-52375-6
Abstract
Recent advances in high-resolution mapping of spatial interactions among regulatory elements support the existence of complex topological assemblies of enhancers and promoters known as enhancer-promoter hubs or cliques. Yet, organization principles of these multi-interacting enhancer-promoter hubs and their potential role in regulating gene expression in cancer remain unclear. Here, we systematically identify enhancer-promoter hubs in breast cancer, lymphoma, and leukemia. We find that highly interacting enhancer-promoter hubs form at key oncogenes and lineage-associated transcription factors potentially promoting oncogenesis of these diverse cancer types. Genomic and optical mapping of interactions among enhancer and promoter elements further show that topological alterations in hubs coincide with transcriptional changes underlying acquired resistance to targeted therapy in T cell leukemia and B cell lymphoma. Together, our findings suggest that enhancer-promoter hubs are dynamic and heterogeneous topological assemblies with the potential to control gene expression circuits promoting oncogenesis and drug resistance.
Siewert Hugelier, Qing Tang, Hannah Hyun-Sook Kim, Melina Theoni Gyparaki, Charles Bond, Adriana Naomi Santiago-Ruiz, Sílvia Porta & Melike Lakadamyali. ECLiPSE: a versatile classification technique for structural and morphological analysis of 2D and 3D single-molecule localization microscopy data. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02414-3
Abstract
Single-molecule localization microscopy (SMLM) has gained widespread use for visualizing the morphology of subcellular organelles and structures with nanoscale spatial resolution. However, analysis tools for automatically quantifying and classifying SMLM images have lagged behind. Here we introduce Enhanced Classification of Localized Point clouds by Shape Extraction (ECLiPSE), an automated machine learning analysis pipeline specifically designed to classify cellular structures captured through two-dimensional or three-dimensional SMLM. ECLiPSE leverages a comprehensive set of shape descriptors, the majority of which are directly extracted from the localizations to minimize bias during the characterization of individual structures. ECLiPSE has been validated using both unsupervised and supervised classification on datasets, including various cellular structures, achieving near-perfect accuracy. We apply two-dimensional ECLiPSE to classify morphologically distinct protein aggregates relevant for neurodegenerative diseases. Additionally, we employ three-dimensional ECLiPSE to identify relevant biological differences between healthy and depolarized mitochondria. ECLiPSE will enhance the way we study cellular structures across various biological contexts.
Yevgeniy Y. Serebrenik, Deepak Mani, Timothé Maujean, George M. Burslem, & Ophir Shalem. Pooled endogenous protein tagging and recruitment for systematic profiling of protein function. Cell Genomics. September 2024. DOI: https://doi.org/10.1016/j.xgen.2024.100651
Summary
Androgen receptor (AR) is a ligand-responsive transcription factor that drives terminal differentiation of the prostatic luminal epithelia. By contrast, in tumors originating from these cells, AR chromatin occupancy is extensively reprogrammed to activate malignant phenotypes, the molecular mechanisms of which remain unknown. Here, we show that tumor-specific AR enhancers are critically reliant on H3K36 dimethyltransferase activity of NSD2. NSD2 expression is abnormally induced in prostate cancer, where its inactivation impairs AR transactivation potential by disrupting over 65% of its cistrome. NSD2-dependent AR sites distinctively harbor the chimeric FOXA1:AR half-motif, which exclusively comprise tumor-specific AR enhancer circuitries defined from patient specimens. NSD2 inactivation also engenders increased dependency on the NSD1 paralog, and a dual NSD1/2 PROTAC degrader is preferentially cytotoxic in AR-dependent prostate cancer models. Altogether, we characterize NSD2 as an essential AR neo-enhanceosome subunit that enables its oncogenic activity, and position NSD1/2 as viable co-targets in advanced prostate cancer.
Jessica C. Lam, Nicholas G. Aboreden, Susannah C. Midla, Siqing Wang, Anran Huang, Cheryl A. Keller, Belinda Giardine, Kate A. Henderson, Ross C. Hardison, Haoyue Zhang, & Gerd Blobel.
YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle. Nature Genetics, 2024. DOI: https://doi.org/10.1038/s41588-024-01871-y
Few transcription factors have been examined for their direct roles in physically connecting enhancers and promoters. Here acute degradation of Yin Yang 1 (YY1) in erythroid cells revealed its requirement for the maintenance of numerous enhancer–promoter loops, but not compartments or domains. Despite its reported ability to interact with cohesin, the formation of YY1-dependent enhancer–promoter loops does not involve stalling of cohesin-mediated loop extrusion. Integrating mitosis-to-G1-phase dynamics, we observed partial retention of YY1 on mitotic chromatin, predominantly at gene promoters, followed by rapid rebinding during mitotic exit, coinciding with enhancer–promoter loop establishment. YY1 degradation during the mitosis-to-G1-phase interval revealed a set of enhancer–promoter loops that require YY1 for establishment during G1-phase entry but not for maintenance in interphase, suggesting that cell cycle stage influences YY1’s architectural function. Thus, as revealed here for YY1, chromatin architectural functions of transcription factors can vary in their interplay with CTCF and cohesin as well as by cell cycle stage.
Titus KR, Simandi Z, Chandrashekar H, Paquet D, Phillips-Cremins JE. Cell-type-specific loops linked to RNA polymerase II elongation in human neural differentiation. Cell Genom. 2024 Aug 14;4(8):100606. doi: 10.1016/j.xgen.2024.100606. Epub 2024 Jul 10. PMID: 38991604; PMCID: PMC11406193.
Abstract
DNA is folded into higher-order structures that shape and are shaped by genome function. The role of long-range loops in the establishment of new gene expression patterns during cell fate transitions remains poorly understood. Here, we investigate the link between cell-specific loops and RNA polymerase II (RNA Pol II) during neural lineage commitment. We find thousands of loops decommissioned or gained de novo upon differentiation of human induced pluripotent stem cells (hiPSCs) to neural progenitor cells (NPCs) and post-mitotic neurons. During hiPSC-to-NPC and NPC-to-neuron transitions, genes changing from RNA Pol II initiation to elongation are >4-fold more likely to anchor cell-specific loops than repressed genes. Elongated genes exhibit significant mRNA upregulation when connected in cell-specific promoter-enhancer loops but not invariant promoter-enhancer loops or promoter-promoter loops or when unlooped. Genes transitioning from repression to RNA Pol II initiation exhibit a slight mRNA increase independent of loop status. Our data link cell-specific loops and robust RNA Pol II-mediated elongation during neural cell fate transitions.
Alessandro Scacchetti, Emily J. Shields, Natalie A. Trigg, Grace S. Lee, Jeremy E. Wilusz, Colin C. Conine, Roberto Bonasio.
A ligation-independent sequencing method reveals tRNA-derived RNAs with blocked 3′ termini. Molecular Cell, 2024, ISSN 1097-2765. DOI: https://doi.org/10.1016/j.molcel.2024.07.008
Despite the numerous sequencing methods available, the diversity in RNA size and chemical modification makes it difficult to capture all RNAs in a cell. We developed a method that combines quasi-random priming with template switching to construct sequencing libraries from RNA molecules of any length and with any type of 3′ modifications, allowing for the sequencing of virtually all RNA species. Our ligation-independent detection of all types of RNA (LIDAR) is a simple, effective tool to identify and quantify all classes of coding and non-coding RNAs. With LIDAR, we comprehensively characterized the transcriptomes of mouse embryonic stem cells, neural progenitor cells, mouse tissues, and sperm. LIDAR detected a much larger variety of tRNA-derived RNAs (tDRs) compared with traditional ligation-dependent sequencing methods and uncovered tDRs with blocked 3′ ends that had previously escaped detection. Therefore, LIDAR can capture all RNAs in a sample and uncover RNA species with potential regulatory functions.
Shin Foong Ngiow, Sasikanth Manne, Yingui Jane Huang, Tarek Azar, Zeyu Chen, Divij Mathew, Qingzhou Chen, Omar Khan, Jennifer E. Wu, Victor Alcalde, Ahron J. Flowers, Sean McClain, Amy E. Baxter, Makoto Kurachi, Junwei Shi, Alexander C. Huang, Josephine R. Giles, Arlene H. Sharp, Dario A.A. Vignali, E. John Wherry. LAG-3 sustains TOX expression and regulates the CD94/NKG2-Qa-1b axis to govern exhausted CD8 T cell NK receptor expression and cytotoxicity. Cell, 2024. DOI: https://doi.org/10.1016/j.cell.2024.07.018
Exhausted CD8 T (Tex) cells in chronic viral infection and cancer have sustained co-expression of inhibitory receptors (IRs). Tex cells can be reinvigorated by blocking IRs, such as PD-1, but synergistic reinvigoration and enhanced disease control can be achieved by co-targeting multiple IRs including PD-1 and LAG-3. To dissect the molecular changes intrinsic when these IR pathways are disrupted, we investigated the impact of loss of PD-1 and/or LAG-3 on Tex cells during chronic infection. These analyses revealed distinct roles of PD-1 and LAG-3 in regulating Tex cell proliferation and effector functions, respectively. Moreover, these studies identified an essential role for LAG-3 in sustaining TOX and Tex cell durability as well as a LAG-3-dependent circuit that generated a CD94/NKG2+ subset of Tex cells with enhanced cytotoxicity mediated by recognition of the stress ligand Qa-1b, with similar observations in humans. These analyses disentangle the non-redundant mechanisms of PD-1 and LAG-3 and their synergy in regulating Tex cells.
HIRA complex deposition of histone H3.3 is driven by histone tetramerization and histone-DNA binding
Austin Vogt, Mary Szurgot, Lauren Gardener, David C. Schultz, Ronen Marmorstein. HIRA complex deposition of histone H3.3 is driven by histone tetramerization and histone-DNA binding. Journal of Biological Chemistry, 2024, 107604, ISSN 0021-9258. DOI: https://doi.org/10.2337/db23-0076
The HIRA histone chaperone complex is comprised of four protein subunits: HIRA, UBN1, CABIN1, and transiently associated ASF1a. All four subunits have been demonstrated to play a role in deposition of the histone variant H3.3 onto areas of actively transcribed euchromatin in cells. The mechanism by which these subunits function together to drive histone deposition has remained poorly understood. Here we present biochemical and biophysical data supporting a model whereby ASF1a delivers histone H3.3/H4 dimers to the HIRA complex, H3.3/H4 tetramerization drives the association of two HIRA/UBN1 complexes, and the affinity of the histones for DNA drives release of ASF1a and subsequent histone deposition. These findings have implications for understanding how other histone chaperone complexes may mediate histone deposition.
Elisabetta Manduchi, Héléne C. Descamps, Jonathan Schug, Tong Da, Deeksha Lahori, Hilana El-Mekkoussi, Michael R. Betts, Klaus H. Kaestner. No evidence for persistent enteroviral B infection of pancreatic islets in type 1 diabetic and pre-diabetic patients from RNA-Seq data. Diabetes. July 26, 2024. DOI: https://doi.org/10.2337/db23-0076
Emily R. Feierman, Sean Louzon, Nicholas A. Prescott, Tracy Biaco, Qingzeng Gao, Qi Qiu, Kyuhyun Choi, Katherine C. Palozola, Anna J. Voss, Shreya D. Mehta, Camille N. Quaye, Katherine T. Lynch, Marc V. Fuccillo, Hao Wu, Yael David, Erica Korb. Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory. Molecular Cell. July 17, 2024. DOI: https://doi.org/10.1016/j.molcel.2024.06.025
Summary
Ting Zhao, Yan Hong, Bowen Yan, Suming Huang, Guo-li Ming, & Hongjun Song. Epigenetic maintenance of adult neural stem cell quiescence in the mouse hippocampus via Setd1a. Nat Commun 15, 5674 (2024). https://doi.org/10.1038/s41467-024-50010-y
Abstract
Quiescence, a hallmark of adult neural stem cells (NSCs), is required for maintaining the NSC pool to support life-long continuous neurogenesis in the adult dentate gyrus (DG). Whether long-lasting epigenetic modifications maintain NSC quiescence over the long term in the adult DG is not well-understood. Here we show that mice with haploinsufficiency of Setd1a, a schizophrenia risk gene encoding a histone H3K4 methyltransferase, develop an enlarged DG with more dentate granule cells after young adulthood. Deletion of Setd1a specifically in quiescent NSCs in the adult DG promotes their activation and neurogenesis, which is countered by inhibition of the histone demethylase LSD1. Mechanistically, RNA-sequencing and CUT & RUN analyses of cultured quiescent adult NSCs reveal Setd1a deletion-induced transcriptional changes and many Setd1a targets, among which down-regulation of Bhlhe40 promotes quiescent NSC activation in the adult DG in vivo. Together, our study reveals a Setd1a-dependent epigenetic mechanism that sustains NSC quiescence in the adult DG.
Phillip Wulfridge & Kavitha Sarma. Intertwining roles of R-loops and G-quadruplexes in DNA repair, transcription and genome organization. Nature Cell Biology, June 24, 2024. DOI: https://doi.org/10.1038/s41556-024-01437-4
Abstract
R-loops are three-stranded nucleic acid structures that are abundant and widespread across the genome and that have important physiological roles in many nuclear processes. Their accumulation is observed in cancers and neurodegenerative disorders. Recent studies have implicated a function for R-loops and G-quadruplex (G4) structures, which can form on the displaced single strand of R-loops, in three-dimensional genome organization in both physiological and pathological contexts. Here we discuss the interconnected functions of DNA:RNA hybrids and G4s within R-loops, their impact on DNA repair and gene regulatory networks, and their emerging roles in genome organization during development and disease.
Hee Jong Kim, Mary R. Szurgot, Trevor van Eeuwen, M. Daniel Ricketts, Pratik Basnet, Athena L. Zhang, Austin Vogt, Samah Sharmin, Craig D. Kaplan, Benjamin A. Garcia, Ronen Marmorstein, Kenji Murakami. Structure of the Hir histone chaperone complex. Molecular Cell, June 25, 2024. DOI: https://doi.org/10.1016/j.molcel.2024.05.031
Summary
Shin-ichi Inoue, Matthew J. Emmett, Hee-Woong Lim, Mohit Midha, Hannah J. Richter, Isaac J. Celwyn, Rashid Mehmood, Maria Chondronikola, Samuel Klein, Amy K. Hauck, Mitchell A. Lazar. Short-term cold exposure induces persistent epigenomic memory in brown fat. Cell Metabolism, June 17, 2024. DOI: https://doi.org/10.1016/j.cmet.2024.05.011
Summary
Shuo Zhang, Benjamin J Heil, Weiguang Mao, Maria Chikina, Casey S Greene, Elizabeth A Heller. MousiPLIER: A Mouse Pathway-Level Information Extractor Model. eNeuro. 2024 Jun 5;11(6):ENEURO.0313-23.2024. doi: 10.1523/ENEURO.0313-23.2024. PMID: 38789274; PMCID: PMC11154669.
Abstract
High-throughput gene expression profiling measures individual gene expression across conditions. However, genes are regulated in complex networks, not as individual entities, limiting the interpretability of gene expression data. Machine learning models that incorporate prior biological knowledge are a powerful tool to extract meaningful biology from gene expression data. Pathway-level information extractor (PLIER) is an unsupervised machine learning method that defines biological pathways by leveraging the vast amount of published transcriptomic data. PLIER converts gene expression data into known pathway gene sets, termed latent variables (LVs), to substantially reduce data dimensionality and improve interpretability. In the current study, we trained the first mouse PLIER model on 190,111 mouse brain RNA-sequencing samples, the greatest amount of training data ever used by PLIER. We then validated the mousiPLIER approach in a study of microglia and astrocyte gene expression across mouse brain aging. mousiPLIER identified biological pathways that are significantly associated with aging, including one latent variable (LV41) corresponding to striatal signal. To gain further insight into the genes contained in LV41, we performed k-means clustering on the training data to identify studies that respond strongly to LV41. We found that the variable was relevant to striatum and aging across the scientific literature. Finally, we built a Web server (http://mousiplier.greenelab.com/) for users to easily explore the learned latent variables. Taken together, this study defines mousiPLIER as a method to uncover meaningful biological processes in mouse brain transcriptomic studies.
Julianna G. Supplee, Hayley C. Affronti, Richard Duan, Rebekah C. Brooks, Zachary E. Stine, Phuong T.T. Nguyen, Laura V. Pinheiro, Michael C. Noji, Jack M. Drummond, Kevin Huang, Kollin Schultz, Chi V. Dang, Ronen Marmorstein, Kathryn E. Wellen. ACLY alternative splicing correlates with cancer phenotypes. Journal of Biological Chemistry, 2024. DOI: https://doi.org/10.1016/j.devcel.2024.05.006
Abstract
ATP-citrate lyase (ACLY) links carbohydrate and lipid metabolism and provides nucleocytosolic acetyl-CoA necessary for protein acetylation. ACLY has two major splice isoforms: the full-length canonical “long” isoform and an uncharacterized “short” isoform in which exon 14 is spliced out. Exon 14 encodes 10 amino acids within a disordered region of the protein and includes at least 1 site that is dynamically phosphorylated. Both isoforms are expressed in healthy tissues to varying degrees. Analysis of human transcriptomic data revealed that the Percent Spliced In (PSI) of exon 14, i.e., the proportion of long isoform, is increased in several cancers and correlated with poorer overall survival in a pan-cancer analysis, though not in individual tumor types, which prompted us to explore potential biochemical and functional differences between ACLY isoforms.
Here, we show that there are no discernible differences in enzymatic activity or stability between isoforms or phosphomutants of ACLY in vitro. Similarly, both isoforms and phosphomutants were able to rescue ACLY functions, including fatty acid synthesis and bulk histone acetylation, when re-expressed in Acly knockout cells. Deletion of Acly exon 14 in mice did not overtly impact development or metabolic physiology, nor did it attenuate tumor burden in a genetic model of intestinal cancer.
Notably, expression of epithelial splicing regulatory protein 1 (ESRP1) is highly correlated with ACLY PSI. We report that ACLY splicing is regulated by ESRP1. In turn, both ESRP1 expression and ACLY PSI are correlated with specific immune signatures in tumors. Despite these intriguing patterns of ACLY splicing in healthy and cancer tissues, functional differences between the isoforms remain elusive.
Avital Swisa, Julia Kieckhaefer, Scott G. Daniel, Hilana El-Mekkoussi, Hannah M. Kolev, Mark Tigue, Chunsheng Jin, Charles-Antonie Assenmacher, Lenka Dohnalová, Chistoph A. Thaiss, Niclas G. Karlsson, Kyle Bittinger, Klaus H. Kaestner. The evolutionarily ancient FOXA transcription factors shape the murine gut microbiome via control of epithelial glycosylation. Developmental Cell, 2024. DOI: https://doi.org/10.1016/j.devcel.2024.05.006
Summary
Han Zhao, Yinzhi Lin, En Lin, Fuhai Liu, Lirong Shu, Dannan Jing, Baiyue Wang, Manzhu Wang, Fengian Shan, Lin Zhang, Jessica C. Lam, Susannah C. Midla, Belinda M. Giardine, Cheryl A. Keller, Ross C. Hardison, Gerd A. Blobel, & Haoyue Zhang. Genome folding principles uncovered in condensin-depleted mitotic chromosomes. Nat Genet (2024). https://doi.org/10.1038/s41588-024-01759-x
During mitosis, condensin activity is thought to interfere with interphase chromatin structures. To investigate genome folding principles in the absence of chromatin loop extrusion, we codepleted condensin I and condensin II, which triggered mitotic chromosome compartmentalization in ways similar to that in interphase. However, two distinct euchromatic compartments, indistinguishable in interphase, emerged upon condensin loss with different interaction preferences and dependencies on H3K27ac. Constitutive heterochromatin gradually self-aggregated and cocompartmentalized with facultative heterochromatin, contrasting with their separation during interphase. Notably, some cis-regulatory element contacts became apparent even in the absence of CTCF/cohesin-mediated structures. Heterochromatin protein 1 (HP1) proteins, which are thought to partition constitutive heterochromatin, were absent from mitotic chromosomes, suggesting, surprisingly, that constitutive heterochromatin can self-aggregate without HP1. Indeed, in cells traversing from M to G1 phase in the combined absence of HP1α, HP1β and HP1γ, constitutive heterochromatin compartments are normally re-established. In sum, condensin-deficient mitotic chromosomes illuminate forces of genome compartmentalization not identified in interphase cells.
Jessica E. Packard, Namrata Kumar, Matthew D. Weitzman, Jill A. Dembowski. Identifying Protein Interactions with Viral DNA Genomes during Virus Infection.
Viruses, 2024, 16(6), 845; https://doi.org/10.3390/v16060845
Kaeli M. Mathias, Yiman Liu, Liling Wan. Dysregulation of transcriptional condensates in human disease: mechanisms, biological functions, and open questions. Genetics & Development (2024). https://doi.org/10.1016/j.gde.2024.102203
Precise gene expression, crucial for normal development and health, depends on the co-ordinated assembly and function of various factors within the crowded nucleus. Recent evidence suggests that this process is in part regulated by mesoscale compartmentalization and concentration of transcriptional components within condensates, offering a new perspective on gene regulation. Dysregulation of transcriptional condensates is increasingly associated with diseases, indicating a potential role in pathogenesis. In this mini-review, we provide a concise overview of the current understanding of the formation and function of transcriptional condensates, with a specific focus on recent advances in their dysregulation and implications in diseases, notably cancer. We also address limitations in the field and highlight open questions for future research.
Michael B. Cory, Allen Li, Christina M. Hurley, Peter J. Carman, Ruth A. Pumroy, Zachary M. Hostetler, Ryann M. Perez, Yarra Venkatesh, Xinning Li, Kushol Gupta, E. James Petersson & Rahul M. Kohli. The LexA–RecA* structure reveals a cryptic lock-and-key mechanism for SOS activation. Nat Struct Mol Biol (2024). https://doi.org/10.1038/s41594-024-01317-3
Abstract
The bacterial SOS response plays a key role in adaptation to DNA damage, including genomic stress caused by antibiotics. SOS induction begins when activated RecA*, an oligomeric nucleoprotein filament that forms on single-stranded DNA, binds to and stimulates autoproteolysis of the repressor LexA. Here, we present the structure of the complete Escherichia coli SOS signal complex, constituting full-length LexA bound to RecA*. We uncover an extensive interface unexpectedly including the LexA DNA-binding domain, providing a new molecular rationale for ordered SOS gene induction. We further find that the interface involves three RecA subunits, with a single residue in the central engaged subunit acting as a molecular key, inserting into an allosteric binding pocket to induce LexA cleavage. Given the pro-mutagenic nature of SOS activation, our structural and mechanistic insights provide a foundation for developing new therapeutics to slow the evolution of antibiotic resistance.
C. C.-S. Hsiung, C. M. Wilson, N. A. Sambold, R. Dai, Q. Chen, N. Teyssier, S. Misiukiewicz, A. Arab, T. O’Loughlin, J. C. Cofsky, J. Shi & L. A. Gilbert. Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations. Nat Biotechnol (2024). https://doi.org/10.1038/s41587-024-02224-0
Abstract
Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting one to three genomic sites per cell. We engineer an Acidaminococcus Cas12a (AsCas12a) variant, multiplexed transcriptional interference AsCas12a (multiAsCas12a), that incorporates R1226A, a mutation that stabilizes the ribonucleoprotein–DNA complex via DNA nicking. The multiAsCas12a-KRAB fusion improves CRISPRi activity over DNase-dead AsCas12a-KRAB fusions, often rescuing the activities of lentivirally delivered CRISPR RNAs (crRNA) that are inactive when used with the latter. multiAsCas12a-KRAB supports CRISPRi using 6-plex crRNA arrays in high-throughput pooled screens. Using multiAsCas12a-KRAB, we discover enhancer elements and dissect the combinatorial function of cis-regulatory elements in human cells. These results instantiate a group testing framework for efficiently surveying numerous combinations of chromatin perturbations for biological discovery and engineering.
Aanchal Mongia, Fatema Tuz Zohora, Noah G. Burget, Yeqiao Zhou, Diane C. Saunders, Yue J. Wang, Marcela Brissova, Alvin C. Powers, Klaus H. Kaestner, Golnaz Vahedi, Ali Naji, Gregory W. Schwartz, and Robert B. Faryabi. AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics. Nat Commun 15, 3744 (2024). https://doi.org/10.1038/s41467-024-47334-0
Abstract
Cellular composition and anatomical organization influence normal and aberrant organ functions. Emerging spatial single-cell proteomic assays such as Image Mass Cytometry (IMC) and Co-Detection by Indexing (CODEX) have facilitated the study of cellular composition and organization by enabling high-throughput measurement of cells and their localization directly in intact tissues. However, annotation of cell types and quantification of their relative localization in tissues remain challenging. To address these unmet needs for atlas-scale datasets like Human Pancreas Analysis Program (HPAP), we develop AnnoSpat (Annotator and Spatial Pattern Finder) that uses neural network and point process algorithms to automatically identify cell types and quantify cell-cell proximity relationships. Our study of data from IMC and CODEX shows the higher performance of AnnoSpat in rapid and accurate annotation of cell types compared to alternative approaches. Moreover, the application of AnnoSpat to type 1 diabetic, non-diabetic autoantibody-positive, and non-diabetic organ donor cohorts recapitulates known islet pathobiology and shows differential dynamics of pancreatic polypeptide (PP) cell abundance and CD8+ T cells infiltration in islets during type 1 diabetes progression.
Abhijeet R. Patil, Jonathan Schug, Chengyang Liu, Deeksha Lahori, Hélène C. Descamps, the Human Pancreas Analysis Consortium, Ali Naji, Klaus H. Kaestner, Robert B. Faryabi, Golnaz Vahedi. Modeling type 1 diabetes progression using machine learning and single-cell transcriptomic measurements in human islets. Cell Reports Medicine. (April 26, 2024). https://doi.org/10.1016/j.xcrm.2024.101535
Summary
Jose A. Martinez-Sarmiento, Maria Pia Cosma, Melike Lakadamyali. Dissecting gene activation and chromatin remodeling dynamics in single human cells undergoing reprogramming. Cell Reports. (May 2, 2024). https://doi.org/10.1016/j.celrep.2024.114170
Summary
Yiman Liu, Qinglan Li, Chujie Gong, Sylvia Tang, Krista A. Budinich, Ashley Vanderbeck, Kaeli M. Mathias, Gerald B. Wertheim, Son C. Nguygen, Riley Outen, Eric F. Joyce, Ivan Maillard, Liling Wan. Condensate-promoting ENL mutation drives tumorigenesis in vivo through dynamic regulation of histone modifications and gene expression. Cancer Discov (2024). https://doi.org/10.1038/s42255-024-01029-4
Abstract
Amy K. Hauck, Rashid Mehmood, Bryce J. Carpenter, Maxwell T. Frankfurter, Michael C. Tackenberg, Shin-ichi Inoue, Maria K. Krieg, Fathima N. Cassim Bawa, Mohit K. Midha, Delaine M. Zundell, Kirill Batmanov, & Mitchell A. Lazar. Nuclear receptor corepressors non-canonically drive glucocorticoid receptor-dependent activation of hepatic gluconeogenesis. Nat Metab (2024). https://doi.org/10.1038/s42255-024-01029-4
Abstract
Nuclear receptor corepressors (NCoRs) function in multiprotein complexes containing histone deacetylase 3 (HDAC3) to alter transcriptional output primarily through repressive chromatin remodelling at target loci. In the liver, loss of HDAC3 causes a marked hepatosteatosis largely because of de-repression of genes involved in lipid metabolism; however, the individual roles and contribution of other complex members to hepatic and systemic metabolic regulation are unclear. Here we show that adult loss of both NCoR1 and NCoR2 (double knockout (KO)) in hepatocytes phenocopied the hepatomegalic fatty liver phenotype of HDAC3 KO. In addition, double KO livers exhibited a dramatic reduction in glycogen storage and gluconeogenic gene expression that was not observed with hepatic KO of individual NCoRs or HDAC3, resulting in profound fasting hypoglycaemia. This surprising HDAC3-independent activation function of NCoR1 and NCoR2 is due to an unexpected loss of chromatin accessibility on deletion of NCoRs that prevented glucocorticoid receptor binding and stimulatory effect on gluconeogenic genes. These studies reveal an unanticipated, non-canonical activation function of NCoRs that is required for metabolic health.
Jordan C. Harris, Natalie A. Trigg, Bruktawit Goshu, Yuichi Yokoyama, Lenka Dohnalová, Ellen K. White, Adele Harman, Sofía M. Murga-Garrido, Jamie Ting-Chun Pan, Preeti Bhanap, Christoph A. Thaiss, Elizabeth A. Grice, Colin C. Conine, Taku Kambayashi. The microbiota and T cells non-genetically modulate inherited phenotypes transgenerationally. Cell Reports, Volume 43, Issue 4 (2024). https://doi.org/10.1038/s41586-024-07278-3
Abstract
The host-microbiota relationship has evolved to shape mammalian physiology, including immunity, metabolism, and development. Germ-free models are widely used to study microbial effects on host processes such as immunity. Here, we find that both germ-free and T cell-deficient mice exhibit a robust sebum secretion defect persisting across multiple generations despite microbial colonization and T cell repletion. These phenotypes are inherited by progeny conceived during in vitro fertilization using germ-free sperm and eggs, demonstrating that non-genetic information in the gametes is required for microbial-dependent phenotypic transmission. Accordingly, gene expression in early embryos derived from gametes from germ-free or T cell-deficient mice is strikingly and similarly altered. Our findings demonstrate that microbial- and immune-dependent regulation of non-genetic information in the gametes can transmit inherited phenotypes transgenerationally in mice. This mechanism could rapidly generate phenotypic diversity to enhance host adaptation to environmental perturbations.
Glennis A. Logsdon, Allison N. Rozanski, Fedor Ryabov, Tamara Potapova, Valery A. Shepelev, Claudia R. Catacchio, David Porubsky, Yafei Mao, DongAhn Yoo, Mikko Rautiainen, Sergey Koren, Sergey Nurk, Julian K. Lucas, Kendra Hoekzema, Katherine M. Munson, Jennifer L. Gerton, Adam M. Phillippy, Mario Ventura, Ivan A. Alexandrov & Evan E. Eichler. The variation and evolution of complete human centromeres. Nature (2024). https://doi.org/10.1038/s41586-024-07278-3
Abstract
Human centromeres have been traditionally very difficult to sequence and assemble owing to their repetitive nature and large size1. As a result, patterns of human centromeric variation and models for their evolution and function remain incomplete, despite centromeres being among the most rapidly mutating regions. Here, using long-read sequencing, we completely sequenced and assembled all centromeres from a second human genome and compared it to the finished reference genome. We find that the two sets of centromeres show at least a 4.1-fold increase in single-nucleotide variation when compared with their unique flanks and vary up to 3-fold in size. Moreover, we find that 45.8% of centromeric sequence cannot be reliably aligned using standard methods owing to the emergence of new α-satellite higher-order repeats (HORs). DNA methylation and CENP-A chromatin immunoprecipitation experiments show that 26% of the centromeres differ in their kinetochore position by >500 kb. To understand evolutionary change, we selected six chromosomes and sequenced and assembled 31 orthologous centromeres from the common chimpanzee, orangutan and macaque genomes. Comparative analyses reveal a nearly complete turnover of α-satellite HORs, with characteristic idiosyncratic changes in α-satellite HORs for each species. Phylogenetic reconstruction of human haplotypes supports limited to no recombination between the short (p) and long (q) arms across centromeres and reveals that novel α-satellite HORs share a monophyletic origin, providing a strategy to estimate the rate of saltatory amplification and mutation of human centromeric DNA.
Rexxi D. Prasasya, Blake A. Caldwell, Zhengfeng Liu, Songze Wu, N. Adrian Leu, Johanna M. Fowler, Steven A. Cincotta, Diana J. Laird, Rahul M. Kohli, and Marisa S. Bartolomei. Iterative oxidation by TET1 is required for reprogramming of imprinting control regions and patterning of mouse sperm hypomethylated regions. Developmental Cell. April 2, 2024. DOI: https://doi.org/10.1016/j.devcel.2024.02.012
Summary
Ten-eleven translocation (TET) enzymes iteratively oxidize 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC), 5-formylcytosine, and 5-carboxylcytosine to facilitate active genome demethylation. Whether these bases are required to promote replication-coupled dilution or activate base excision repair during mammalian germline reprogramming remains unresolved due to the inability to decouple TET activities. Here, we generated two mouse lines expressing catalytically inactive TET1 (Tet1-HxD) and TET1 that stalls oxidation at 5hmC (Tet1-V). Tet1 knockout and catalytic mutant primordial germ cells (PGCs) fail to erase methylation at select imprinting control regions and promoters of meiosis-associated genes, validating the requirement for the iterative oxidation of 5mC for complete germline reprogramming. TET1V and TET1HxD rescue most hypermethylation of Tet1−/− sperm, suggesting the role of TET1 beyond its oxidative capability. We additionally identify a broader class of hypermethylated regions in Tet1 mutant mouse sperm that depend on TET oxidation for reprogramming. Our study demonstrates the link between TET1-mediated germline reprogramming and sperm methylome patterning.
Craig W. Gambogi, Gabriel J. Birchak, Elie Mer, David M. Brown, George Yankson, Kathryn Kixmoeller, Janardan N. Gavade, Josh L. Espinoza, Prakriti Kashyap, Chris L. Duypont, Glennis A. Logsdon, Patrick Heun, John I. Glass, and Ben E. Black. Efficient formation of single-copy human artificial chromosomes. Science383,1344-1349(2024). DOI:10.1126/science.adj3566
Abstract
Abstract
The physical basis of phase separation is thought to consist of the same types of bonds that specify conventional macromolecular interactions yet is unsatisfyingly often referred to as ‘fuzzy’. Gaining clarity on the biogenesis of membraneless cellular compartments is one of the most demanding challenges in biology. Here, we focus on the chromosome passenger complex (CPC), that forms a chromatin body that regulates chromosome segregation in mitosis. Within the three regulatory subunits of the CPC implicated in phase separation – a heterotrimer of INCENP, Survivin, and Borealin – we identify the contact regions formed upon droplet formation using hydrogen/deuterium-exchange mass spectrometry (HXMS). These contact regions correspond to some of the interfaces seen between individual heterotrimers within the crystal lattice they form. A major contribution comes from specific electrostatic interactions that can be broken and reversed through initial and compensatory mutagenesis, respectively. Our findings reveal structural insight for interactions driving liquid-liquid demixing of the CPC. Moreover, we establish HXMS as an approach to define the structural basis for phase separation.
Karen G. Wong, Yu-Chia F. Cheng, Vincent H. Wu, Anna A. Kiselva, Jun Li, Andrey Poleshko, Cheryl M. Smith, and Jonathan A. Eptstein.Growth factor–induced activation of MSK2 leads to phosphorylation of H3K9me2S10 and corresponding changes in gene expression.Sci. Adv.10,eadm9518(2024).DOI:10.1126/sciadv.adm9518
Abstract
Gabriela Hayward-Lara, Matthew D Fischer, and Mustafa Mir. Dynamic microenvironments shape nuclear organization and gene expression. Current Opinion in Genetics & Development. Volume 86, 2024. 102177. ISSN 0959-437X. https://doi.org/10.1016/j.gde.2024.102177.
Highlights
- Microenvironments are local high concentrations of multiple nuclear factors.
- Microenvironments form due to protein–protein and protein–chromatin interactions.
- Local concentrations of protein modulate binding frequency rather than duration.
- Microenvironments can bridge multiple genes and regulatory elements.
- Microenvironment lifetimes vary and correlate with regulatory function.
Live imaging has revealed that the regulation of gene expression is largely driven by transient interactions. For example, many regulatory proteins bind chromatin for just seconds, and loop-like genomic contacts are rare and last only minutes. These discoveries have been difficult to reconcile with our canonical models that are predicated on stable and hierarchical interactions. Proteomic microenvironments that concentrate nuclear factors may explain how brief interactions can still mediate gene regulation by creating conditions where reactions occur more frequently. Here, we summarize new imaging technologies and recent discoveries implicating microenvironments as a potential driver of nuclear function. Finally, we propose that key properties of proteomic microenvironments, such as their size, enrichment, and lifetimes, are directly linked to regulatory function.
Arun Padmanabhan, T. Yvanka de Soysa, Angelo Pelonero, Valerie Sapp, Parisha P. Shah, Qiaohong Wang, Li Li, Clara Youngna Lee, Nandhini Sadagopan, Tomohiro Nishino, Lin Ye, Rachel Yang, Ashley Karnay, Andrey Poleshko, Nikhita Bolar, Ricardo Linares-Saldana, Sanjeev S. Ranade, Michael Alexanian, Sarah U. Morton, Mohit Jain, Saptarsi M. Haldar, Deepak Srivastava, Rajan Jain. A genome-wide CRISPR screen identifies BRD4 as a regulator of cardiomyocyte differentiation. Nat Cardiovasc Res (2024). https://doi.org/10.1038/s44161-024-00431-1
Abstract
Human induced pluripotent stem cell (hiPSC) to cardiomyocyte (CM) differentiation has reshaped approaches to studying cardiac development and disease. In this study, we employed a genome-wide CRISPR screen in a hiPSC to CM differentiation system and reveal here that BRD4, a member of the bromodomain and extraterminal (BET) family, regulates CM differentiation. Chemical inhibition of BET proteins in mouse embryonic stem cell (mESC)-derived or hiPSC-derived cardiac progenitor cells (CPCs) results in decreased CM differentiation and persistence of cells expressing progenitor markers. In vivo, BRD4 deletion in second heart field (SHF) CPCs results in embryonic or early postnatal lethality, with mutants demonstrating myocardial hypoplasia and an increase in CPCs. Single-cell transcriptomics identified a subpopulation of SHF CPCs that is sensitive to BRD4 loss and associated with attenuated CM lineage-specific gene programs. These results highlight a previously unrecognized role for BRD4 in CM fate determination during development and a heterogenous requirement for BRD4 among SHF CPCs.
Katherine S. Forsyth, Nikhil Jiwrajka, Claudia D. Lovell, Natalie E. Toothacre, Montserrat C. Anguera. The conneXion between sex and immune responses. Nat Rev Immunol (2024). https://doi.org/10.1038/s41577-024-00996-9
Abstract
There are notable sex-based differences in immune responses to pathogens and self-antigens, with female individuals exhibiting increased susceptibility to various autoimmune diseases, and male individuals displaying preferential susceptibility to some viral, bacterial, parasitic and fungal infections. Although sex hormones clearly contribute to sex differences in immune cell composition and function, the presence of two X chromosomes in female individuals suggests that differential gene expression of numerous X chromosome-linked immune-related genes may also influence sex-biased innate and adaptive immune cell function in health and disease. Here, we review the sex differences in immune system composition and function, examining how hormones and genetics influence the immune system. We focus on the genetic and epigenetic contributions responsible for altered X chromosome-linked gene expression, and how this impacts sex-biased immune responses in the context of pathogen infection and systemic autoimmunity.
Kiara N Berríos, Aleksia Barka, Jasleen Gill, Juan C Serrano, Peter F Bailer, Jared B Parker, Niklaus H Evitt, Kiran S Gajula, Junwei Shi, Rahul M Kohli, Cooperativity between Cas9 and hyperactive AID establishes broad and diversifying mutational footprints in base editors, Nucleic Acids Research, 2024;, gkae024, https://doi.org/10.1093/nar/gkae024
Abstract
The partnership of DNA deaminase enzymes with CRISPR-Cas nucleases is now a well-established method to enable targeted genomic base editing. However, an understanding of how Cas9 and DNA deaminases collaborate to shape base editor (BE) outcomes has been lacking. Here, we support a novel mechanistic model of base editing by deriving a range of hyperactive activation-induced deaminase (AID) base editors (hBEs) and exploiting their characteristic diversifying activity. Our model involves multiple layers of previously underappreciated cooperativity in BE steps including: (i) Cas9 binding can potentially expose both DNA strands for ‘capture’ by the deaminase, a feature that is enhanced by guide RNA mismatches; (ii) after strand capture, the intrinsic activity of the DNA deaminase can tune window size and base editing efficiency; (iii) Cas9 defines the boundaries of editing on each strand, with deamination blocked by Cas9 binding to either the PAM or the protospacer and (iv) non-canonical edits on the guide RNA bound strand can be further elicited by changing which strand is nicked by Cas9. Leveraging insights from our mechanistic model, we create novel hBEs that can remarkably generate simultaneous C > T and G > A transitions over >65 bp with significant potential for targeted gene diversification.
Daniel C. Xu, Hanna Sas-Nowosielska, Greg Donahue, Hua Huang, Naemeh Pourshafie, Charly R. Good & Shelley L. Berger. Histone acetylation in an Alzheimer’s disease cell model promotes homeostatic amyloid-reducing pathways. acta neuropathol commun 12, 3 (2024). https://doi.org/10.1186/s40478-023-01696-6
Abstract
Alzheimer’s Disease (AD) is a disorder characterized by cognitive decline, neurodegeneration, and accumulation of amyloid plaques and tau neurofibrillary tangles in the brain. Dysregulation of epigenetic histone modifications may lead to expression of transcriptional programs that play a role either in protecting against disease genesis or in worsening of disease pathology. One such histone modification, acetylation of histone H3 lysine residue 27 (H3K27ac), is primarily localized to genomic enhancer regions and promotes active gene transcription. We previously discovered H3K27ac to be more abundant in AD patient brain tissue compared to the brains of age-matched non-demented controls. In this study, we use iPSC-neurons derived from familial AD patients with an amyloid precursor protein (APP) duplication (APPDup neurons) as a model to study the functional effect of lowering CBP/P300 enzymes that catalyze H3K27ac. We found that homeostatic amyloid-reducing genes were upregulated in the APPDup neurons compared to non-demented controls. We lowered CBP/P300 to reduce H3K27ac, which led to decreased expression of numerous of these homeostatic amyloid-reducing genes, along with increased extracellular secretion of a toxic amyloid-β species, Aβ(1–42). Our findings suggest that epigenomic histone acetylation, including H3K27ac, drives expression of compensatory genetic programs in response to AD-associated insults, specifically those resulting from APP duplication, and thus may play a role in mitigating AD pathology in neurons.
Malachowski T, Chandradoss KR, Boya R, Zhou L, Cook AL, Su C, Pham K, Haws SA, Kim JH, Ryu HS, Ge C, Luppino JM, Nguyen SC, Titus KR, Gong W, Wallace O, Joyce EF, Wu H, Rojas LA, Phillips-Cremins JE. Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome. Cell. 2023 Dec 21;186(26):5840-5858.e36. doi: 10.1016/j.cell.2023.11.019. PMID: 38134876; PMCID: PMC10794044.
Abstract
Short tandem repeat (STR) instability causes transcriptional silencing in several repeat expansion disorders. In fragile X syndrome (FXS), mutation-length expansion of a CGG STR represses FMR1 via local DNA methylation. Here, we find megabase-scale H3K9me3 domains on autosomes and encompassing FMR1 on the X chromosome in FXS patient-derived iPSCs, iPSC-derived neural progenitors, EBV-transformed lymphoblasts, and brain tissue with mutation-length CGG expansion. H3K9me3 domains connect via inter-chromosomal interactions and demarcate severe misfolding of TADs and loops. They harbor long synaptic genes replicating at the end of S phase, replication-stress-induced double-strand breaks, and STRs prone to stepwise somatic instability. CRISPR engineering of the mutation-length CGG to premutation length reverses H3K9me3 on the X chromosome and multiple autosomes, refolds TADs, and restores gene expression. H3K9me3 domains can also arise in normal-length iPSCs created with perturbations linked to genome instability, suggesting their relevance beyond FXS. Our results reveal Mb-scale heterochromatinization and trans interactions among loci susceptible to instability.
Eun Kyung Ko, Amy Anderson, Carina D’souza, Jonathan Zou, Sijia Huang, Sohyun Cho, Faizan Alawi, Stephen Prouty, Vivian Lee, Sora Yoon, Keegan Krick, Yoko Horiuchi, Kai Ge, John T. Seykora, Brian C. Capell. Disruption of H3K36 methylation provokes cellular plasticity to drive aberrant glandular formation and squamous carcinogenesis. Developmental Cell. January 9, 2024. doi: https://doi.org/10.1016/j.devcel.2023.12.007.
Highlights
• Disruption of H3K36 methylation via H3K36M expression drives epithelial plasticity
• This triggers epithelial glandulogenesis while also increasing cancer susceptibility
• H3K36M rewires the global and genome-wide H3K36me2 and H3K27me3 epigenetic landscape
• These chromatin changes suppress differentiation genes while activating glandular genes
Summary
Chromatin organization is essential for maintaining cell-fate trajectories and developmental programs. Here, we find that disruption of H3K36 methylation dramatically impairs normal epithelial differentiation and development, which promotes increased cellular plasticity and enrichment of alternative cell fates. Specifically, we observe a striking increase in the aberrant generation of excessive epithelial glandular tissues, including hypertrophic salivary, sebaceous, and meibomian glands, as well as enhanced squamous tumorigenesis. These phenotypic and gene expression manifestations are associated with loss of H3K36me2 and rewiring of repressive H3K27me3, changes we also observe in human patients with glandular hyperplasia. Collectively, these results have identified a critical role for H3K36 methylation in both in vivo epithelial cell-fate decisions and the prevention of squamous carcinogenesis and suggest that H3K36 methylation modulation may offer new avenues for the treatment of numerous common disorders driven by altered glandular function, which collectively affect large segments of the human population.
Gambogi CW, Pandey N, Dawicki-McKenna JM, Arora UP, Liskovykh MA, Ma J, Lamelza P, Larionov V, Lampson MA, Logsdon GA, Dumont BL, Black BE. Centromere innovations within a mouse species. Sci Adv. 2023 Nov 17;9(46):eadi5764. doi: 10.1126/sciadv.adi5764. Epub 2023 Nov 15. PMID: 37967185; PMCID: PMC10651114.
Abstract
Mammalian centromeres direct faithful genetic inheritance and are typically characterized by regions of highly repetitive and rapidly evolving DNA. We focused on a mouse species, Mus pahari, that we found has evolved to house centromere-specifying centromere protein-A (CENP-A) nucleosomes at the nexus of a satellite repeat that we identified and termed π-satellite (π-sat), a small number of recruitment sites for CENP-B, and short stretches of perfect telomere repeats. One M. pahari chromosome, however, houses a radically divergent centromere harboring ~6 mega-base pairs of a homogenized π-sat-related repeat, π-satB, that contains >20,000 functional CENP-B boxes. There, CENP-B abundance promotes accumulation of microtubule-binding components of the kinetochore and a microtubule-destabilizing kinesin of the inner centromere. We propose that the balance of pro- and anti-microtubule binding by the new centromere is what permits it to segregate during cell division with high fidelity alongside the older ones whose sequence creates a markedly different molecular composition.
Timothe Maujean, Prakash Kannaboina, Adam I Green, and George Burslem. Lead-Oriented Synthesis of Epigenetic Relevant Scaffolds. Chemical Communications. 15 Nov 2023. https://doi.org/10.1039/D3CC04317G
Abstract
A simple and rationale method to rank molecules’ lead-likeness using continuous evaluation functions was hereby developed. This strategy proved to be competitive against known methods and finally helped driving synthetic efforts towards candidates of interest for epigenetic applications towards HDAC6, BRD4 and EZH2
Michelle Y.Y. Lee, Klaus H. Kaestner, Mingyao Li. Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data. Genome Biol 24, 244 (2023). https://doi.org/10.1186/s13059-023-03073-x
Abstract
Background
Single-cell RNA-sequencing (scRNA-seq) measures gene expression in single cells, while single-nucleus ATAC-sequencing (snATAC-seq) quantifies chromatin accessibility in single nuclei. These two data types provide complementary information for deciphering cell types and states. However, when analyzed individually, they sometimes produce conflicting results regarding cell type/state assignment. The power is compromised since the two modalities reflect the same underlying biology. Recently, it has become possible to measure both gene expression and chromatin accessibility from the same nucleus. Such paired data enable the direct modeling of the relationships between the two modalities. Given the availability of the vast amount of single-modality data, it is desirable to integrate the paired and unpaired single-modality datasets to gain a comprehensive view of the cellular complexity.
Results
We benchmark nine existing single-cell multi-omic data integration methods. Specifically, we evaluate to what extent the multiome data provide additional guidance for analyzing the existing single-modality data, and whether these methods uncover peak-gene associations from single-modality data. Our results indicate that multiome data are helpful for annotating single-modality data. However, we emphasize that the availability of an adequate number of nuclei in the multiome dataset is crucial for achieving accurate cell type annotation. Insufficient representation of nuclei may compromise the reliability of the annotations. Additionally, when generating a multiome dataset, the number of cells is more important than sequencing depth for cell type annotation.
Conclusions
Seurat v4 is the best currently available platform for integrating scRNA-seq, snATAC-seq, and multiome data even in the presence of complex batch effects.
Telomouse—a mouse model with human-length telomeres generated by a single amino acid change in RTEL1
Linyang Ju, Karl M. Glastad, Lihong Sheng, Janko Gospocic, Callum J. Kingwell, Shawn M. Davidson, Sarah D. Kocher, Roberto Bonasio, Shelley L. Berger. Hormonal gatekeeping via the blood-brain barrier governs caste-specific behavior in ants. Cell. September 7, 2023. DOI: https://doi.org/10.1016/j.cell.2023.08.002.
Abstract
Telomeres, the ends of eukaryotic chromosomes, protect genome integrity and enable cell proliferation. Maintaining optimal telomere length in the germline and throughout life limits the risk of cancer and enables healthy aging. Telomeres in the house mouse, Mus musculus, are about five times longer than human telomeres, limiting the use of this common laboratory animal for studying the contribution of telomere biology to aging and cancer. We identified a key amino acid variation in the helicase RTEL1, naturally occurring in the short-telomere mouse species M. spretus. Introducing this variation into M. musculus is sufficient to reduce the telomere length set point in the germline and generate mice with human-length telomeres. While these mice are fertile and appear healthy, the regenerative capacity of their colonic epithelium is compromised. The engineered Telomouse reported here demonstrates a dominant role of RTEL1 in telomere length regulation and provides a unique model for aging and cancer.
Linyang Ju, Karl M. Glastad, Lihong Sheng, Janko Gospocic, Callum J. Kingwell, Shawn M. Davidson, Sarah D. Kocher, Roberto Bonasio, Shelley L. Berger. Hormonal gatekeeping via the blood-brain barrier governs caste-specific behavior in ants. Cell. September 7, 2023. DOI: https://doi.org/10.1016/j.cell.2023.08.002.
Summary
Here, we reveal an unanticipated role of the blood-brain barrier (BBB) in regulating complex social behavior in ants. Using scRNA-seq, we find localization in the BBB of a key hormone-degrading enzyme called juvenile hormone esterase (Jhe), and we show that this localization governs the level of juvenile hormone (JH3) entering the brain. Manipulation of the Jhe level reprograms the brain transcriptome between ant castes. Although ant Jhe is retained and functions intracellularly within the BBB, we show that Drosophila Jhe is naturally extracellular. Heterologous expression of ant Jhe into the Drosophila BBB alters behavior in fly to mimic what is seen in ants. Most strikingly, manipulation of Jhe levels in ants reprograms complex behavior between worker castes. Our study thus uncovers a remarkable, potentially conserved role of the BBB serving as a molecular gatekeeper for a neurohormonal pathway that regulates social behavior.
Phillip Wulfridge, Qingqing Yan, Nathaniel Rell, John Doherty, Skye Jacobson, Sarah Offley, Sandra Deliard, Kelly Feng, Jennifer E. Phillips-Cremins, Alessandro Gardini, Kavitha Sarma. G-quadruplexes associated with R-loops promote CTCF binding. Molecular Cell. Volume 82, Issue 17. P3064-3079.E5, August 7, 2023. DOI: https://doi.org/10.1016/j.molcel.2023.07.009
Summary
Alexandra M. Maldonado López, Eun Kyung Ko, Sijia Huang, Gina Pacella, Nina Kuprasertkul, Carina A. D’Souza, Raúl A. Reyes Hueros, Hui Shen, Julian Stoute, Heidi Elashal, Morgan Sinkfield, Amy Anderson, Stephen Pourty, Hua-Bing Li, John T. Seykora, Kathy Fange Liu, Brian C. Capell. Mettl3-catalyzed m6A regulates histone modifier and modification expression in self-renewing somatic tissue.Sci. Adv.9,eadg5234(2023).DOI:10.1126/sciadv.adg5234
Abstract
Abstract
Centromeres direct genetic inheritance but are not themselves genetically encoded. Instead, centromeres are defined epigenetically by the presence of a histone H3 variant, CENP-A.1 In cultured somatic cells, an established paradigm of cell-cycle-coupled propagation maintains centromere identity: CENP-A is partitioned between sisters during replication and replenished by new assembly, which is restricted to G1. The mammalian female germ line challenges this model because of the cell-cycle arrest between pre-meiotic S phase and the subsequent G1, which can last for the entire reproductive lifespan (months to decades). New CENP-A chromatin assembly maintains centromeres during prophase I in worm and starfish oocytes,2,3 suggesting that a similar process may be required for centromere inheritance in mammals. To test this hypothesis, we developed an oocyte-specific conditional knockout (cKO) mouse for Mis18α, an essential component of the assembly machinery. We find that embryos derived from Mis18α knockout oocytes fail to assemble CENP-A nucleosomes prior to zygotic genome activation (ZGA), validating the knockout model. We show that deletion of Mis18α in the female germ line at the time of birth has no impact on centromeric CENP-A nucleosome abundance, even after 6-8 months of aging. In addition, there is no detectable detriment to fertility. Thus, centromere chromatin is maintained long-term, independent of new assembly during the extended prophase I arrest in mouse oocytes.
Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects
Abstract
Oxidative modification of 5-methylcytosine (5mC) by ten-eleven translocation (TET) DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve 5mC and 5hmC, leaving the cell-type-specific regulatory mechanisms of TET and 5hmC largely unknown. Here, we present joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq), a scalable and quantitative approach that simultaneously profiles 5hmC and true 5mC in single cells by harnessing differential deaminase activity of APOBEC3A toward 5mC and chemically protected 5hmC. Joint-snhmC-seq profiling of single nuclei from mouse brains reveals an unprecedented level of epigenetic heterogeneity of both 5hmC and true 5mC at single-cell resolution. We show that cell-type-specific profiles of 5hmC or true 5mC improve multimodal single-cell data integration, enable accurate identification of neuronal subtypes and uncover context-specific regulatory effects on cell-type-specific genes by TET enzymes.
Abstract
In development, pioneer transcription factors access silent chromatin to reveal lineage-specific gene programs. The structured DNA-binding domains of pioneer factors have been well characterized, but whether and how intrinsically disordered regions affect chromatin and control cell fate is unclear. Here, we report that deletion of an intrinsically disordered region of the pioneer factor TCF-1 (termed L1) leads to an early developmental block in T cells. The few T cells that develop from progenitors expressing TCF-1 lacking L1 exhibit lineage infidelity distinct from the lineage diversion of TCF-1-deficient cells. Mechanistically, L1 is required for activation of T cell genes and repression of GATA2-driven genes, normally reserved to the mast cell and dendritic cell lineages. Underlying this lineage diversion, L1 mediates binding of TCF-1 to its earliest target genes, which are subject to repression as T cells develop. These data suggest that the intrinsically disordered N terminus of TCF-1 maintains T cell lineage fidelity.
Abstract
The human genome functions as a three-dimensional chromatin polymer, driven by a complex collection of chromosome interactions. Although the molecular rules governing these interactions are being quickly elucidated, relatively few proteins regulating this process have been identified. Here, to address this gap, we developed high-throughput DNA or RNA labelling with optimized Oligopaints (HiDRO)—an automated imaging pipeline that enables the quantitative measurement of chromatin interactions in single cells across thousands of samples. By screening the human druggable genome, we identified more than 300 factors that influence genome folding during interphase. Among these, 43 genes were validated as either increasing or decreasing interactions between topologically associating domains. Our findings show that genetic or chemical inhibition of the ubiquitous kinase GSK3A leads to increased long-range chromatin looping interactions in a genome-wide and cohesin-dependent manner. These results demonstrate the importance of GSK3A signalling in nuclear architecture and the use of HiDRO for identifying mechanisms of spatial genome organization.
Mutant NPM1 hijacks transcriptional hub to maintain pathogenic gene programs in acute myeloid leukemia.Wang X*, Fan D*, Han Q*, Liu Y*, Miao H, Wang X, Li Q, Chen D, Gore H, Himadewi P, Pfeifer GP, Cierpicki T, Grembecka J, Su J, Chong S#, Wan L#, Zhang X#. Cancer Discovery https://doi.org/10.1158/2159-8290.CD-22-0424. (*co-first; #co-corresponding)
A pioneer factor locally opens compacted chromatin to enable targeted ATP-dependent nucleosome remodeling Frederick MA, Williamson KE, Garcia MF, Ferretti MB, McCarthy RL, Donahue G, Monteiro EL, Takenaka N, Reynaga J, Kadoch C, Zaret KS. Nat Struct Mol Biol. 2022 Dec 19; doi: 10.1038/s41594-022-00886-5
CTCF blocks antisense transcription initiation at divergent promoters.
Luan J, Vermunt MW, Syrett CM, Coté A, Tome JM, Zhang H, Huang A, Luppino JM, Keller CA, Giardine BM, Zhang S, Dunagin MC, Zhang Z, Joyce EF, Lis JT, Raj A, Hardison RC, Blobel GA. Nat Struct Mol Biol. 2022 Nov;29(11):1136-1144. doi: 10.1038/s41594-022-00855-y. Epub 2022 Nov 11. PMID: 36369346
Cell-type specific profiling of histone post-translational modifications in the adult mouse striatum
Marco D Carpenter, Delaney K Fischer, Shuo Zhang, Allison M Bond, Kyle S Czarnecki, Morgan T Woolf, Hongjun Song, Elizabeth A Heller. Cell-type specific profiling of histone post-translational modifications in the adult mouse striatum. Nat Commun. 2022 Dec 13;13(1):7720. doi: 10.1038/s41467-022-35384-1. Erratum in: Nat Commun. 2023 Feb 22;14(1):987. doi: 10.1038/s41467-023-36768-7. PMID: 36513652; PMCID: PMC9747932.
Abstract
Epigenetic gene regulation in the heterogeneous brain remains challenging to decipher with current strategies. Bulk tissue analysis from pooled subjects reflects the average of cell-type specific changes across cell-types and individuals, which obscures causal relationships between epigenetic modifications, regulation of gene expression, and complex pathology. To address these limitations, we optimized a hybrid protocol, ICuRuS, for the isolation of nuclei tagged in specific cell-types and histone post translational modification profiling from the striatum of a single mouse. We combined affinity-based isolation of the medium spiny neuron subtypes, Adenosine 2a Receptor or Dopamine Receptor D1, with cleavage of histone-DNA complexes using an antibody-targeted micrococcal nuclease to release DNA complexes for paired end sequencing. Unlike fluorescence activated cell sorting paired with chromatin immunoprecipitation, ICuRuS allowed for robust epigenetic profiling at cell-type specific resolution. Our analysis provides a framework to understand combinatorial relationships between neuronal-subtype-specific epigenetic modifications and gene expression.
Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer. Song L*, Yao X*, Li H, Peng B, Boka AP, Liu Y, Chen G, Liu Z, Mathias KM, Xia L, Li Q, Mir M, Li Y#, Li H#, Wan L#. Molecular Cell, 2022 Nov 3;82(21):4080-4098.e12. (featured in cover) PMID:36272410 (*co-first;#co-corresponding)
Delaney K Fischer, Keegan S Krick, Chloe Han, Morgan T Woolf, Elizabeth A Heller. Cocaine regulation of Nr4a1 chromatin bivalency and mRNA in male and female mice. Sci Rep. 2022 Sep 21;12(1):15735. doi: 10.1038/s41598-022-19908-9. PMID: 36130958; PMCID: PMC9492678.
Abstract
Cocaine epigenetically regulates gene expression via changes in histone post-translational modifications (HPTMs). We previously found that the immediate early gene Nr4a1 is epigenetically activated by cocaine in mouse brain reward regions. However, few studies have examined multiple HPTMs at a single gene. Bivalent gene promoters are simultaneously enriched in both activating (H3K4me3 (K4)) and repressive (H3K27me3 (K27)) HPTMs. As such, bivalent genes are lowly expressed but poised for activity-dependent gene regulation. In this study, we identified K4&K27 bivalency at Nr4a1 following investigator-administered cocaine in male and female mice. We applied sequential chromatin immunoprecipitation and qPCR to define Nr4a1 bivalency and expression in striatum (STR), prefrontal cortex (PFC), and hippocampus (HPC). We used Pearson’s correlation to quantify relationships within each brain region across treatment conditions for each sex. In female STR, cocaine increased Nr4a1 mRNA while maintaining Nr4a1 K4&K27 bivalency. In male STR, cocaine enriched repressive H3K27me3 and K4&K27 bivalency at Nr4a1 and maintained Nr4a1 mRNA. Furthermore, cocaine epigenetically regulated a putative NR4A1 target, Cartpt, in male PFC. This study defined the epigenetic regulation of Nr4a1 in reward brain regions in male and female mice following cocaine, and, thus, shed light on the biological relevance of sex to cocaine use disorder.
Small-molecule inhibition of the acyl-lysine reader ENL as a strategy against acute myeloid leukemia
Small-molecule inhibition of the acyl-lysine reader ENL as a strategy against acute myeloid leukemia. Liu Y, Li H, Alikarami F, Barrett DR, Khan TA, Michino M, Hill C, Mahdavi L, Song L, Tang S, Yang L, Li Y, Pokharel SP, Li Q, Stamford AW, Liverton N, Renzetti LM, Taylor S, Watt GF, Ladduwahetty T, Kargman S, Meinke PT, Foley MA, Shi J, Li H, Chen CW, Gardini A, Huggins DJ, Bernt KM#, Wan L#. Cancer Discovery, September 2022.
Quantitative sub-cellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation. Trefely S, Huber K, Liu J Noji M, Stransky S, Singh J, Doan MT, Lovell CD,von Krusenstiern E, Jiang H, Bostwick A, Pepper HL, Izzo L, Zhao Z, Xu JP, Bedi Jr KC, Rame JE, Bogner-Strauss J, Mesaros C, Sidoli S, Wellen KE*,Snyder NW*. Mol Cell, Jan 20;82(2):447-462 *co-corresponding authors
Neuronal YY1 in the prefrontal cortex regulates transcriptional and behavioral responses to chronic stress. Kwon DY, Xu B#, Hu P#, Zhao Y-T, Beagan JA, Nofziger JH, Cui Y, Phillips-Cremins JE, Blendy JA, Wu H, Zhou Z*. Nature Communications 13: 55. doi.org/10.1038/s41467-021-27571-3, 2022.
Berríos KN, Evitt NH, DeWeerd RA, Ren D, Luo M, Barka A, Wang T, Bartman CR, Lan Y, Green AM, Shi J, Kohli RM. Controllable genome editing with split-engineered base editors. Nat Chem Biol. 2021 Oct 18. doi: 10.1038/s41589-021-00880-w. Epub ahead of print. PMID: 34663942.
Temporal manipulation of Cdkl5 reveals essential post-developmental functions and reversible CDKL5 deficiency disorder-related deficits. Terzic B, Davatolhagh MF, Ho Y, Tang S, Liu Y-T, Xia Z, Cui Y, Fuccillo MV and Zhou Z*. Journal of Clinical Investigation 131(20): e143655, 2021.
Temporal manipulation of Cdkl5 reveals essential post-developmental functions and reversible CDKL5 deficiency disorder-related deficits. Terzic B, Davatolhagh MF, Ho Y, Tang S, Liu Y-T, Xia Z, Cui Y, Fuccillo MV and Zhou Z*. Journal of Clinical Investigation 131(20): e143655, 2021.
Linares-Saldana R, Kim W, Bolar NA, Zhang H, Koch-Bojalad BA, Yoon S, Shah PP, Karnay A, Park DS, Luppino JM, Nguyen SC, Padmanabhan A, Smith CL, Poleshko A, Wang Q, Li L, Srivastava D, Vahedi G, Eom GH, Blobel GA, Joyce EF, Jain R. BRD4 orchestrates genome folding to promote neural crest differentiation. Nat Genet. 2021 Oct;53(10):1480-1492. doi: 10.1038/s41588-021-00934-8. Epub 2021 Oct 5. PMID: 34611363.
Glastad KM, Ju L, Berger SL. PLoS Genet. 2021 Sep 22;17(9):e1009801. doi: 10.1371/journal.pgen.1009801. PMID: 34550980; PMCID: PMC8489709.
Mellis IA, Edelstein HI, Truitt R, Goyal Y, Beck LE, Symmons O, Dunagin MC, Linares Saldana RA, Shah PP, Pérez-Bermejo JA, Padmanabhan A, Yang W, Jain R, Raj A. Cell Syst. 2021 Sep 22;12(9):885-899.e8. doi: 10.1016/j.cels.2021.07.003. Epub 2021 Aug 4. PMID: 34352221.
Single-molecule tracking technologies for quantifying the dynamics of gene regulation in cells, tissue, and embryos.
A.P. Boka, A. Mukherjee, M. Mir. Development 148(18): dev199744, September 2021.
Song-Jun Xu, Sonia I Lombroso, Delaney K Fischer, Marco D Carpenter, Dylan M Marchione, Peter J Hamilton, Carissa J Lim, Rachel L Neve, Benjamin A Garcia, Mathieu E Wimmer, R Christopher Pierce, Elizabeth A Heller. Chromatin-mediated alternative splicing regulates cocaine-reward behavior. Neuron. 2021 Sep 15;109(18):2943-2966.e8. doi: 10.1016/j.neuron.2021.08.008. Epub 2021 Sep 3. PMID: 34480866; PMCID: PMC8454057.
Abstract
Neuronal alternative splicing is a key gene regulatory mechanism in the brain. However, the spliceosome machinery is insufficient to fully specify splicing complexity. In considering the role of the epigenome in activity-dependent alternative splicing, we and others find the histone modification H3K36me3 to be a putative splicing regulator. In this study, we found that mouse cocaine self-administration caused widespread differential alternative splicing, concomitant with the enrichment of H3K36me3 at differentially spliced junctions. Importantly, only targeted epigenetic editing can distinguish between a direct role of H3K36me3 in splicing and an indirect role via regulation of splice factor expression elsewhere on the genome. We targeted Srsf11, which was both alternatively spliced and H3K36me3 enriched in the brain following cocaine self-administration. Epigenetic editing of H3K36me3 at Srsf11 was sufficient to drive its alternative splicing and enhanced cocaine self-administration, establishing the direct causal relevance of H3K36me3 to alternative splicing of Srsf11 and to reward behavior.
Blobel GA, Higgs DR, Mitchell JA, Notani D, Young RA. Testing the super-enhancer concept. Nat Rev Genet. 2021 Sep 3. doi: 10.1038/s41576-021-00398-w. Epub ahead of print. PMID: 34480110.
Zhang H, Lam J, Zhang D, Lan Y, Vermunt MW, Keller CA, Giardine B, Hardison RC, Blobel GA. Nat Commun. 2021;12:5157. doi: 10.1038/s41467-021-25418-5.
Schwartz GW, Zhou Y, Petrovic J, Pear WS, Faryabi RB. Cell Rep. 2021;36(8):109575. doi: 10.1016/j.celrep.2021.109575. PMID: 34433064.
Green A and Burslem GM. RSC Med Chem. 2021; Accepted Manuscript. doi: 10.1039/D1MD00193K
Aleman JR, Kuhn TM, Pascual-Garcia P, Gospocic J, Lan Y, Bonasio R, Little SC, Capelson M. Cell Rep. 2021 Jun 15;35(11):109236. doi: 10.1016/j.celrep.2021.109236. PMID: 34133927.
Smith CL, Poleshko A, Epstein JA. Nucleic Acids Res. 2021 May 22:gkab392. doi: 10.1093/nar/gkab392. Epub ahead of print. PMID: 34023908
Alexander KA, Coté A, Nguyen SC, Zhang L, Gholamalamdari O, Agudelo-Garcia P, Lin-Shiao E, Tanim KMA, Lim J, Biddle N, Dunagin MC, Good CR, Mendoza MR, Little SC, Belmont A, Joyce EF, Raj A, Berger SL. Mol Cell. 2021 Apr 15;81(8):1666-1681.e6. doi: 10.1016/j.molcel.2021.03.006. Epub 2021 Apr 5. PMID: 33823140
Shah PP, Lv W, Rhoades JH, Poleshko A, Abbey D, Caporizzo MA, Linares-Saldana R, Heffler JG, Sayed N, Thomas D, Wang Q, Stanton LJ, Bedi K, Morley MP, Cappola TP, Owens AT, Margulies KB, Frank DB, Wu JC, Rader DJ, Yang W, Prosser BL, Musunuru K, Jain R. Cell Stem Cell. 2021 May 6;28(5):938-954.e9. doi: 10.1016/j.stem.2020.12.016. Epub 2021 Feb 1. PMID: 33529599
Deng Q, Rasool RU, Russell RM, Natesan R, Asangani IA. iScience. 2021 Mar 19;24(3):102254. doi: 10.1016/j.isci.2021.102254. Epub 2021 Mar 1. PMID: 33681723
Pandey N, Black BE. Trends Biochem Sci. 2021 Mar 2:S0968-0004(21)00028-1. doi: 10.1016/j.tibs.2021.01.014. Epub ahead of print. PMID: 33674152
Caldwell BA, Liu MY, Prasasya RD, Wang T, DeNizio JE, Leu NA, Amoh NYA, Krapp C, Lan Y, Shields EJ, Bonasio R, Lengner CJ, Kohli RM, Bartolomei MS. Mol Cell. 2021 Feb 18;81(4):859-869.e8. doi: 10.1016/j.molcel.2020.11.045. Epub 2020 Dec 21. PMID: 33352108
Luan J, Xiang G, Gómez-García PA, Tome JM, Zhang Z, Vermunt MW, Zhang H, Huang A, Keller CA, Giardine BM, Zhang Y, Lan Y, Lis JT, Lakadamyali M, Hardison RC, Blobel GA. Cell Rep. 2021 Feb 23;34(8):108783. doi: 10.1016/j.celrep.2021.108783. PMID: 33626344
Reizel Y, Morgan A, Gao L, Schug J, Mukherjee S, García MF, Donahue G, Baur JA, Zaret KS, Kaestner KH. Dev Cell. 2021 Feb 24:S1534-5807(21)00116-7. doi: 10.1016/j.devcel.2021.02.005. Epub ahead of print. PMID: 33636105
Chen Z, Arai E, Khan O, Zhang Z, Ngiow SF, He Y, Huang H, Manne S, Cao Z, Baxter AE, Cai Z, Freilich E, Ali MA, Giles JR, Wu JE, Greenplate AR, Hakeem MA, Chen Q, Kurachi M, Nzingha K, Ekshyyan V, Mathew D, Wen Z, Speck NA, Battle A, Berger SL, Wherry EJ, Shi J. Cell. 2021 Feb 25:S0092-8674(21)00169-0. doi: 10.1016/j.cell.2021.02.019. Epub ahead of print. PMID: 33636129
Jin R, Klasfeld S, Zhu Y, Fernandez Garcia M, Xiao J, Han SK, Konkol A, Wagner D. Nat Commun. 2021 Jan 27;12(1):626. doi: 10.1038/s41467-020-20883-w. PMID: 33504790
Verma P, Zhou Y, Cao Z, Deraska PV, Deb M, Arai E, Li W, Shao Y, Puentes L, Li Y, Patankar S, Mach RH, Faryabi RB, Shi J, Greenberg RA. Nat Cell Biol. 2021 Jan 18. doi: 10.1038/s41556-020-00624-3. Epub ahead of print. PMID: 33462394
Torre EA, Arai E, Bayatpour S, Jiang CL, Beck LE, Emert BL, Shaffer SM, Mellis IA, Fane ME, Alicea GM, Budinich KA, Weeraratna AT, Shi J, Raj A. Nat Genet. 2021;53(1):76-85. doi: 10.1038/s41588-020-00749-z. Epub 2021 Jan 4. PMID: 33398196
Lan X, Ren R, Feng R, Ly LC, Lan Y, Zhang Z, Aboreden N, Qin K, Horton JR, Grevet JD, Mayuranathan T, Abdulmalik O, Keller CA, Giardine B, Hardison RC, Crossley M, Weiss MJ, Cheng X, Shi J, Blobel GA. Mol Cell. 2020:S1097-2765(20)30784-X. doi: 10.1016/j.molcel.2020.11.006. Online ahead of print. PMID: 33301730
Wu Y, Wang H, Zhang F, Zheng Z, Phillips-Cremins JE, Deary IJ, McRae AF, Wray NR, Zeng J, Yang J. Nat Commun. 2020;11(1):2061. doi: 10.1038/s41467-020-15587-0. PMID: 32345984
Beagan JA, Pastuzyn ED, Fernandez LR, Guo MH, Feng K, Titus KR, Chandrashekar H, Shepherd JD, Phillips-Cremis JE. Nat Neurosci. 2020;23(6):707-717. doi: 10.1038/s41593-020-0634-6. PMID: 32451484
Fernandez LR, Gilgenast TG, Phillips-Cremins JE. Genome Biology. 2020;21(1):219. doi: 10.1186/s13059-020-02061-9. PMID: 32859248
Reizel Y, Morgan A, Gao L, Lan Y, Manduchi E, Waite EL, Wang AW, Wells A, Kaestner KH. Genes Dev. 2020;34(15-16):1039-1050. doi: 10.1101/gad.337691.120. PMID: 32561546
Avrahami D, Wang YJ, Schug J, Feleke E, Gao L, Liu C; HPAP Consortium, Naji A, Glaser B, Kaestner KH. Mol Metab. 2020;42:101057. doi: 10.1016/j.molmet.2020.101057.PMID: 32739450
Zhao S, Jang C, Liu J, Uehara K, Gilbert M, Izzo L, Zeng X, Trefely S, Fernandez S, Carrer A, Miller KD, Schug ZT, Snyder NW, Gade TP, Titchenell PM, Rabinowitz JD, Wellen KE. Nature. 2020;579(7800):586-591. doi: 10.1038/s41586-020-2101-7. PMID: 32214246
Price AM, Hayer KE, McIntyre ABR, Gokhale NS, Abebe JS, Fera AND, Mason CE, Horner SM, Wilson AC, Depledge DP, Weitzman MD. Nat Commun. 2020;11(1):6016. doi: 10.1038/s41467-020-19787-6. PMID: 33243990
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He C, Bozler J, Janssen KA, Wilusz JE, Garcia BA, Schorn AJ, Bonasio R. Nat Struct Mol Biol. 2020. doi: 10.1038/s41594-020-00526-w. PMID: 33230319
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Huang P, Peslak SA, Lan X, Khandros E, Yano JA, Sharma M, Keller CA, Giardine B, Qin K, Abdulmalik O, Hardison RC, Shi J, Blobel GA. Blood. 2020;135(24):2121-2132. doi: 10.1182/blood.2020005301. PMID: 32299090
Nativio R, Lan Y, Donahue G, Sidoli S, Berson A, Srinivasan AR, Shcherbakova O, Amlie-Wolf A, Nie J, Cui X, He C, Wang LS, Garcia BA, Trojanowski JQ, Bonini NM, Berger SL. Nat Genet. 2020;52(10):1024-1035. doi: 10.1038/s41588-020-0696-0. PMID: 32989324
Vrooman LA, Rhon-Calderon EA, Chao OY, Nguyen DK, Narapareddy L, Dahiya AK, Putt ME, Schultz RM, Bartolomei MS. Development. 2020;147(11):dev186551. doi: 10.1242/dev.186551. PMID: 32471820
Bartolomei MS, Oakey RJ, Wutz A. PLoS Genet. 2020 Aug 6;16(8):e1008970. doi: 10.1371/journal.pgen.1008970. PMID: 32760145
Syrett CM, Sierra I, Beethem ZT, Dubin AH, Anguera MC. J Autoimmun. 2020;107:102357. doi: 10.1016/j.jaut.2019.102357. PMID: 31780316
Egervari G, Glastad KM, Berger SL. Science. 2020;370(657):660-662. doi: 10.1126/science.abb4367.
Zhu Y, Klasfeld S, Jeong CW, Jin R, Goto K, Yamaguchi N, Wagner D. Nat Commun. 2020;11(1):5118. doi: 10.1038/s41467-020-18782-1. PMID: 33046692
Qiu Q, Hu P, Qiu X, Govek KW, Cámara PG, Wu H. Nat Methods. 2020 Aug 31. doi: 10.1038/s41592-020-0935-4. PMID: 32868927
Zhang D, Huang P, Sharma M, Keller CA, Giardine B, Zhang H, Gilgenast TG, Phillips-Cremins JE, Hardison RC, Blobel GA. Nat Genet. 2020 Aug 31. doi: 10.1038/s41588-020-0680-8. PMID: 32868908
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Qiwen Hu, Casey S Greene, Elizabeth A Heller. Specific histone modifications associate with alternative exon selection during mammalian development. Nucleic Acids Res. 2020 May 21;48(9):4709-4724. doi: 10.1093/nar/gkaa248. PMID: 32319526; PMCID: PMC7229819.
Abstract
Alternative splicing (AS) is frequent during early mouse embryonic development. Specific histone post-translational modifications (hPTMs) have been shown to regulate exon splicing by either directly recruiting splice machinery or indirectly modulating transcriptional elongation. In this study, we hypothesized that hPTMs regulate expression of alternatively spliced genes for specific processes during differentiation. To address this notion, we applied an innovative machine learning approach to relate global hPTM enrichment to AS regulation during mammalian tissue development. We found that specific hPTMs, H3K36me3 and H3K4me1, play a role in skipped exon selection among all the tissues and developmental time points examined. In addition, we used iterative random forest model and found that interactions of multiple hPTMs most strongly predicted splicing when they included H3K36me3 and H3K4me1. Collectively, our data demonstrated a link between hPTMs and alternative splicing which will drive further experimental studies on the functional relevance of these modifications to alternative splicing.
Zandarashvili L, Langelier MF, Velagapudi UK, Hancock MA, Steffen JD, Billur R, Hannan ZM, Wicks AJ, Krastev DB, Pettitt SJ, Lord CJ, Talele TT, Pascal JM, Black BE. Science. 2020;368(6486). pii: eaax6367. doi: 10.1126/science.aax6367. PMID:32241924
Iwafuchi M, Cuesta I, Donahue G, Takenaka N, Osipovich AB, Magnuson MA, Roder H, Seeholzer SH, Santisteban P, Zaret KS. Nat Genet. 2020. doi: 10.1038/s41588-020-0591-8. [Epub ahead of print]. PMID:32203463
Schwartz GW, Zhou Y, Petrovic J, Fasolino M, Xu L, Shaffer SM, Pear WS, Vahedi G, Faryabi RB. Nat Methods. 2020. doi: 10.1038/s41592-020-0748-5. PMID:32123397
Wang W, Fasolino M, Cattau B, Goldman N, Kong W, Frederick MA, McCright SJ, Kiani K, Fraietta JA, Vahedi G. Proc. Natl. Acad. Sci. U.S.A. 2020;201919259. doi: 10.1073/pnas.1919259117.
Fasolino M, Goldman N, Wang W, Cattau B, Zhou Y, Petrovic J, Link VM, Cote A, Chandra A, Silverman M, Joyce EF, Little SC; HPAP Consortium, Kaestner KH, Naji A, Raj A, Henao-Mejia J, Faryabi RB, Vahedi G. Immunity. 2020. pii: S1074-7613(20)30030-3. doi: 10.1016/j.immuni.2020.01.003. [Epub ahead of print]
Carpenter MD, Hu Q, Bond AM, Lombroso SI, Czarnecki KS, Lim CJ, Song H, Wimmer ME, Pierce RC, Heller EA. Nat Commun. 2020;11(504). doi: 110.1038/s41467-020-14331-y.
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Abstract
Arabidopsis (Arabidopsis thaliana) floral meristems terminate after the carpel primordia arise. This is achieved through the temporal repression of WUSCHEL (WUS), which is essential for stem cell maintenance. At floral stage 6, WUS is repressed by KNUCKLES (KNU), a repressor directly activated by AGAMOUS. KNU was suggested to repress WUS through histone deacetylation; however, how the changes in the chromatin state of WUS are initiated and maintained to terminate the floral meristem remains elusive. Here, we show that KNU integrates initial transcriptional repression with polycomb-mediated stable silencing of WUS After KNU is induced, it binds to the WUS promoter and causes eviction of SPLAYED, which is a known activator of WUS and can oppose polycomb repression. KNU also physically interacts with FERTILIZATION-INDEPENDENT ENDOSPERM, a key polycomb repressive complex2 component, and mediates the subsequent deposition of the repressive histone H3 lysine 27 trimethylation for stable silencing of WUS This multi-step silencing of WUS leads to the termination of floral stem cells, ensuring proper carpel development. Thus, our work describes a detailed mechanism for heritable floral stem cell termination in a precise spatiotemporal manner.
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SAMHD1 Modulates Early Steps during Human Cytomegalovirus Infection by Limiting NF-κB Activation. Kim ET, Roche KL, Kulej K, Spruce LA, Seeholzer SH, Coen DM, Diaz-Griffero F, Murphy EA, Weitzman MD. Cell Rep. 2019 Jul 9;28(2):434-448.e6. doi: 10.1016/j.celrep.2019.06.027. PMID:31291579
LADL: light-activated dynamic looping for endogenous gene expression control.
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Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells
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Choreographing the Double Strand Break Response: Ubiquitin and SUMO Control of Nuclear Architecture. Harding SM, Greenberg RA. Front Genet. 2016 Jun 7;7:103. doi: 10.3389/fgene.2016.00103. eCollection 2016.
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lncRHOXF1, a Long Noncoding RNA from the X Chromosome That Suppresses Viral Response Genes during Development of the Early Human Placenta. Penkala I, Wang J, Syrett CM, Goetzl L, López CB, Anguera MC. Mol Cell Biol. 2016 May 31;36(12):1764-75. doi: 10.1128/MCB.01098-15. Print 2016 Jun 15.
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Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. Beagan JA1, Gilgenast TG1, Kim J1, Plona Z1, Norton HK1, Hu G1, Hsu SC2, Shields EJ2, Lyu X3, Apostolou E4, Hochedlinger K4, Corces VG3, Dekker J5, Phillips Cremins JE6. Cell Stem Cell. 2016 May 5; 18(5):611-24. doi: 10.1016/j.stem.2016.04.004
A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics. Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA. Mol Cell Proteomics. 2016 Jul;15(7):2462-75. doi: 10.1074/mcp.O115.049627. Epub 2016 Apr 25.
Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping. Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA. Mol Cell. 2016 Apr 21;62(2):237-47. doi: 10.1016/j.molcel.2016.03.007. Epub 2016 Apr 7.
Tagging methyl-CpG-binding domain proteins reveals different spatiotemporal expression and supports distinct functions. Wood KH, Johnson BS, Welsh SA, Lee JY, Cui Y, Krizman E, Brodkin ES, Blendy JA, Robinson MB, Bartolomei MS, Zhou Z. Epigenomics. 2016 Apr;8(4):455-73. doi: 10.2217/epi-2015-0004. Epub 2016 Apr 12.
The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation. Iwafuchi-Doi M, Donahue G, Kakumanu A, Watts JA, Mahony S, Pugh BF, Lee D, Kaestner KH, Zaret KS. Mol Cell. 2016 Apr 7;62(1):79-91. doi: 10.1016/j.molcel.2016.03.001.
Long-Term Retention of CENP-A Nucleosomes in Mammalian Oocytes Underpins Transgenerational Inheritance of Centromere Identity. Smoak EM, Stein P, Schultz RM, Lampson MA, Black BE. Curr Biol. 2016 Apr 25;26(8):1110-6. doi: 10.1016/j.cub.2016.02.061. Epub 2016 Mar 31.
CENP-C directs a structural transition of CENP-A nucleosomes mainly through sliding of DNA gyres. Falk SJ, Lee J, Sekulic N, Sennett MA, Lee TH, Black BE. Nat Struct Mol Biol. 2016 Mar;23(3):204-208. doi: 10.1038/nsmb.3175. Epub 2016 Feb 15.
Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X. Wang J, Syrett CM, Kramer MC, Basu A, Atchison ML, Anguera MC. Proc Natl Acad Sci U S A. 2016 Apr 5;113(14):E2029-38. doi: 10.1073/pnas.1520113113. Epub 2016 Mar 21.
The Nuclear Receptor Rev-erbα Regulates Adipose Tissue-specific FGF21 Signaling. Jager J, Wang F, Fang B, Lim HW, Peed LC, Steger DJ, Won KJ, Kharitonenkov A, Adams AC, Lazar MA. J Biol Chem. 2016 May 13;291(20):10867-75. doi: 10.1074/jbc.M116.719120. Epub 2016 Mar 21.
A dynamic intron retention program in the mammalian megakaryocyte and erythrocyte lineages. Edwards CR, Ritchie W, Wong JJ, Schmitz U, Middleton R, An X, Mohandas N, Rasko JE, Blobel GA. Blood. 2016 Mar 9. pii: blood-2016-01-692764
Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss of imprinting mutant. Ginard, P., Kalish, J.M., Jiang, C.L., Yu, A.C., Bartolomei, M.S.* and A. Raj*. (2016). Genes and Development, 30:567-578
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Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells. Gonzales-Cope M, Sidoli S, Bhanu NV, Won KJ, Garcia BA. BMC Genomics. 2016 Feb 4;17:95. doi: 10.1186/s12864-016-2414-y.
MLL1 is essential for the senescence-associated secretory phenotype. Capell BC, Drake AM, Zhu J, Shah PP, Dou Z, Dorsey J, Simola DF, Donahue G, Sammons M, Rai TS, Natale C, Ridky TW, Adams PD, Berger SL. Genes Dev. 2016 Feb 1;30(3):321-36. doi: 10.1101/gad.271882.115.
Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation. Bhanu NV, Sidoli S, Garcia BA. Proteomics. 2016 Feb;16(3):448-58. doi: 10.1002/pmic.201500231. Epub 2016 Jan 28.
From Endoderm to Liver Bud: Paradigms of Cell Type Specification and Tissue Morphogenesis. Ken Zaret. Curr Top Dev Biol. 2016;117:647-69. doi: 10.1016/bs.ctdb.2015.12.015. Epub 2016 Jan 21.
Tet2 Catalyzes Stepwise 5-Methlycytosine Oxidation by an Iterative and de novo Mechanism. Crawford DJ, Liu MY, Nabel CS, Cao XJ, Garcia BA, Kohli RM. J Am Chem Soc. 2016 Jan 27;138(3):730-3. doi: 10.1021/jacs.5b10554. Epub 2016 Jan 13.
The N-terminal Acetyltransferase Naa10/ARD1 Does Not Acetylate Lysine Residues. Magin RS, March ZM, Marmorstein R. J Biol Chem. 2016 Mar 4;291(10):5270-7. doi: 10.1074/jbc.M115.709428. Epub 2016 Jan 11.
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Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus. Simola DF, Graham RJ, Brady CM, Enzmann BL, Desplan C, Ray A, Zwiebel LJ, Bonasio R, Reinberg D, Liebig J, Berger SL. Science. 2016 Jan 1;351(6268):aac6633. doi: 10.1126/science.aac6633.
Mammalian autophagy degrades nuclear constituents in response to tumorigenic stress. Dou Z, Ivanov A, Adams PD, Berger SL. Autophagy. 2016 Aug 2;12(8):1416-7. doi: 10.1080/15548627.2015.1127465. Epub 2015 Dec 10.
H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes. Becker JS, Nicetto D, Zaret KS. Trends Genet. 2016 Jan;32(1):29-41. doi: 10.1016/j.tig.2015.11.001. Epub 2015 Dec 8. Review.
Autophagy mediates degradation of nuclear lamina. Dou Z, Xu C, Donahue G, Shimi T, Pan JA, Zhu J, Ivanov A, Capell BC, Drake AM, Shah PP, Catanzaro JM, Daniel Ricketts M, Lamark T, Adam SA, Marmorstein R, Zong WX, Johansen T, Goldman RD, Adams PD, Berger SL. Nature. 2015 Nov 5;527(7576):105-9. doi: 10.1038/nature15548. Epub 2015 Oct 28.
PMID: 26524528
AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis. Yamaguchi N, Jeong CW, Nole-Wilson S, Krizek BA, Wagner D. Plant Physiol. 2016 Jan;170(1):283-93. doi: 10.1104/pp.15.00969. Epub 2015 Nov 4.
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Science editor’s choice (https://stke.sciencemag.org/content/7/325/ec127)
http://www.eurekalert.org/pub_releases/2014-05/uop-phh050814.php
Optical Measurement of Cell Cycle Dependent Growth. M. Mir, Z. Wang, Z. Shen, M. Bednarz, R. Bashir, I. Golding and G. Popescu. Proceedings of the National Academies of Sciences (PNAS) 108 (32): 13124-13129, 2011.
MERIT40 controls BRCA1-Rap80 complex integrity and recruitment to DNA double-strand breaks. Shao G, Patterson-Fortin J, Messick TE, Feng D, Shanbhag N, Wang Y, Greenberg RA. Genes Dev. 2009 Mar 15;23(6):740-54. doi: 10.1101/gad.1739609. Epub 2009 Mar 4. PMID: 19261746
The Rap80-BRCC36 de-ubiquitinating enzyme complex antagonizes RNF8-Ubc13-dependent ubiquitination events at DNA double strand breaks. Shao G, Lilli DR, Patterson-Fortin J, Coleman KA, Morrissey DE, Greenberg RA. Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3166-71. doi: 10.1073/pnas.0807485106. Epub 2009 Feb 6. PMID: 19202061