bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2025–07–27
twenty-six papers selected by
Connor Rogerson, University of Cambridge
  1. The SWI/SNF-related protein SMARCA3 is a histone H3K23 ubiquitin ligase that regulates H3K9me3 in cancer.
  2. Epigenetic priming of mammalian embryonic enhancer elements coordinates developmental gene networks.
  3. β-catenin functions as a molecular adapter for disordered cBAF interactions.
  4. BAHCC1 promotes gene expression in neuronal cells by antagonizing SIN3A-HDAC1.
  5. Chromatin architecture mapping by multiplex proximity tagging.
  6. NKX2-1 drives neuroendocrine transdifferentiation of prostate cancer via epigenetic and 3D chromatin remodeling.
  7. SMAdd-seq: probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing.
  8. Dissecting the enhancer gene regulatory network in early Drosophila spermatogenesis.
  9. The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate.
  10. Joint representation and visualization of derailed cell states with Decipher.
  11. Spatial-scERA: a method for reconstructing spatial single-cell enhancer activity in multicellular organisms.
  12. A STAT3/integrin axis accelerates pancreatic cancer initiation and progression.
  13. Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte development.
  14. Structural mechanism of H3K27 demethylation and crosstalk with heterochromatin markers.
  15. G-quadruplexes are promoter elements controlling nucleosome exclusion and RNA polymerase II pausing.
  16. High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer.
  17. E2F activity determines mitosis versus whole-genome duplication in G2-arrested cells.
  18. The invasion phenotypes of glioblastoma depend on plastic and reprogrammable cell states.
  19. Combined single-cell profiling of chromatin-transcriptome and splicing across brain cell types, regions and disease state.
  20. PPARG-centric transcriptional re-wiring during differentiation of human trophoblast stem cells into extravillous trophoblasts.
  21. The histone H3 lysine 36 demethylase KDM2A/FBXL11 controls Polycomb-mediated gene repression and germ cell development in male mice.
  22. Single-molecule live imaging of subunit interactions and exchange within cellular regulatory complexes.
  23. Leveraging chromatin packing domains to target chemoevasion in vivo.
  24. Modeling combinatorial regulation from single-cell multi-omics provides regulatory units underpinning cell type landscape using cRegulon.
  25. A phage transcription factor displaces the host σ factor and stabilizes its own σ factor.
  26. Deciphering direct transcriptional effects of epigenetic compounds through large-scale new RNA profiling.
  1. Mol Cell. 2025 Jul 12. pii: S1097-2765(25)00550-7. [Epub ahead of print]
    The SWI/SNF-related protein SMARCA3 is a histone H3K23 ubiquitin ligase that regulates H3K9me3 in cancer.
    Ifé Akano, Jakob M Hebert, Rochelle L Tiedemann, Qingzeng Gao, Yang Xiao, Nicholas A Prescott, Yanqing Liu, Kay See Tan, Ryan M Bastle, Aarthi Ramakrishnan, Ian Maze, Simone Sidoli, Richard P Koche, Karuna Ganesh, Scott B Rothbart, Yael David.
      Histone ubiquitination is a crucial post-translational modification (PTM) regulating chromatin function, yet many histone ubiquitination sites and the enzymes that control them remain poorly understood. Here, we identify SMARCA3, a SWI/SNF-related protein frequently downregulated in colorectal cancer (CRC), as an E3 ubiquitin ligase that targets histone H3 at lysine 23 (H3K23). We demonstrate that SMARCA3 histone ubiquitination activity is stimulated by the repressive H3K9me3 mark. Loss of SMARCA3 reduces both H3K23Ub and H3K9me3, increasing chromatin accessibility at promoters and enhancers enriched for pioneer transcription factor motifs. This chromatin "rewiring" alters the transcriptional landscape, driving upregulation of cancer-promoting genes. We validate this mechanism in CRC cell lines and patient-derived organoids, where SMARCA3 loss reduces H3K23Ub and H3K9me3. In xenograft mouse models, overexpression of wild-type SMARCA3, but not a RING domain mutant, suppresses tumor growth. Together, our findings define SMARCA3 as a key chromatin regulator contributing to CRC pathogenesis through epigenetic mechanisms.
    Keywords:  epigenetics, histone, ubiquitination, methylation, chromatin, accessibility, cancer, RING, E3 ligase
    DOI:  https://doi.org/10.1016/j.molcel.2025.06.020
  2. Genome Biol. 2025 Jul 18. 26(1): 214
    Epigenetic priming of mammalian embryonic enhancer elements coordinates developmental gene networks.
    Christopher D Todd, Jannat Ijaz, Fereshteh Torabi, Oleksandr Dovgusha, Stephen Bevan, Olivia Cracknell, Tim Lohoff, Stephen Clark, Ricard Argelaguet, Juliette Pierce, Ioannis Kafetzopoulos, Alice Santambrogio, Jennifer Nichols, Ferdinand von Meyenn, Ufuk Günesdogan, Stefan Schoenfelder, Wolf Reik.
       BACKGROUND: Embryonic development requires the accurate spatiotemporal execution of cell lineage-specific gene expression programs, which are controlled by transcriptional enhancers. Developmental enhancers adopt a primed chromatin state prior to their activation. How this primed enhancer state is established and maintained and how it affects the regulation of developmental gene networks remains poorly understood.
    RESULTS: Here, we use comparative multi-omic analyses of human and mouse early embryonic development to identify subsets of postgastrulation lineage-specific enhancers which are epigenetically primed ahead of their activation, marked by the histone modification H3K4me1 within the epiblast. We show that epigenetic priming occurs at lineage-specific enhancers for all three germ layers and that epigenetic priming of enhancers confers lineage-specific regulation of key developmental gene networks. Surprisingly in some cases, lineage-specific enhancers are epigenetically marked already in the zygote, weeks before their activation during lineage specification. Moreover, we outline a generalizable strategy to use naturally occurring human genetic variation to delineate important sequence determinants of primed enhancer function.
    CONCLUSIONS: Our findings identify an evolutionarily conserved program of enhancer priming and begin to dissect the temporal dynamics and mechanisms of its establishment and maintenance during early mammalian development.
    Keywords:  Cell fate; Developmental biology; Embryogenesis; Enhancers; Epigenetics; Multi-omics
    DOI:  https://doi.org/10.1186/s13059-025-03658-8
  3. Mol Cell. 2025 Jul 15. pii: S1097-2765(25)00576-3. [Epub ahead of print]
    β-catenin functions as a molecular adapter for disordered cBAF interactions.
    Yuen San Chan, Qinyu Gao, Sarah A Robinson, Wenzhi Wang, Ruzena Filandrova, Lisa-Maria Weinhold, Mario Loeza Cabrera, Miao Zhang, Chandra Shekar R Ambati, Antonio M Lerario, Nagireddy Putluri, Katja Kiseljak-Vassiliades, Margaret E Wierman, Mouhammed Amir Habra, Gary D Hammer, Vaclav Veverka, Katerina Cermakova, H Courtney Hodges.
      BAF (SWI/SNF) chromatin remodelers engage binding partners to generate site-specific DNA accessibility. However, the basis for interaction between BAF and divergent binding partners has remained unclear. Here, we tested the hypothesis that scaffold proteins augment BAF's binding repertoire by examining β-catenin (CTNNB1) and steroidogenic factor 1 (SF-1, NR5A1), a transcription factor central to steroid production in human cells. BAF inhibition rapidly opposed SF-1/β-catenin enhancer occupancy, impairing SF-1 target activation and SF-1/β-catenin autoregulation. These effects arise due to β-catenin's role as a molecular adapter between SF-1 and an intrinsically disordered region (IDR) of the canonical BAF (cBAF) subunit ARID1A. In contrast to exclusively IDR-driven mechanisms, adapter function is mediated by direct association of ARID1A with β-catenin's folded Armadillo repeats. β-catenin similarly linked cBAF to YAP1, SOX2, FOXO3, and CBP/p300, reflecting a general IDR-mediated mechanism for modular coordination between factors. Molecular visualization highlights β-catenin's adapter role for interaction of cBAF with binding partners.
    Keywords:  IDRs; adrenocortical carcinoma; chromatin remodeling; co-activators; scaffold proteins; steroid hormones; transcription factors; transcription regulators; unstructured protein
    DOI:  https://doi.org/10.1016/j.molcel.2025.06.026
  4. Nucleic Acids Res. 2025 Jul 19. pii: gkaf650. [Epub ahead of print]53(14):
    BAHCC1 promotes gene expression in neuronal cells by antagonizing SIN3A-HDAC1.
    Alan Monziani, Rotem Ben-Tov Perry, Hadas Hezroni, Igor Ulitsky.
      Chromatin modifications play a key role in regulating gene expression during development and adult physiology. Histone acetylation, particularly H3K27ac, is associated with increased activity of gene regulatory elements such as enhancers and promoters. However, the regulation of the machinery that writes, reads, and erases this modification remains poorly understood. In particular, the SIN3A-HDAC1 complex possesses histone deacetylase activity, yet it commonly resides at active regulatory regions. Here, we study BAHCC1, a large chromatin-associated protein essential for viability and recently reported to play a largely repressive role. We show that in neuronal lineage cells, BAHCC1 is mainly associated with regulatory elements marked with H3K27ac. BAHCC1 interacts and co-occupies shared genomic regions with the SIN3A scaffold protein, but not with its paralog SIN3B, and its perturbations lead to altered acetylation and expression of proximal genes in a neuronal cell line and primary cortical neurons. The regulated genes are enriched for those functioning in neurogenesis and cell migration, and primary cortical neurons with reduced Bahcc1 expression display impaired neurite outgrowth. We thus propose a model in which BAHCC1 antagonizes SIN3A histone deacetylation and positively regulates the expression of genes that are important for growth and migration-related processes in the neuronal lineage.
    DOI:  https://doi.org/10.1093/nar/gkaf650
  5. Mol Cell. 2025 Jul 17. pii: S1097-2765(25)00547-7. [Epub ahead of print]85(14): 2796-2811.e5
    Chromatin architecture mapping by multiplex proximity tagging.
    Axel Delamarre, Benton Bailey, Jennifer Yavid, Richard Koche, Neeman Mohibullah, Iestyn Whitehouse.
      Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed a proximity-tagging method to map molecules that associate in 3D space. Using this method-PCP (proximity copy paste)-we mapped the positioning and connectivity of individual nucleosomes in Saccharomyces cerevisiae. We show that chromatin is predominantly organized into regularly spaced nucleosome arrays that can be positioned or delocalized. PCP can also map long-range, multi-way interactions, and we provide direct evidence supporting a model that metaphase chromosomes are compacted by cohesin loop clustering. Analyzing single-molecule nuclease footprinting data, we define distinct chromatin states within a mixed population to show that non-canonical overlapping di-nucleosomes are a stable feature of chromatin. PCP is a versatile method, allowing the detection of the connectivity of individual molecules locally and over large distances to be mapped at high resolution in a single experiment.
    Keywords:  OLDN; PCP; cohesin; nucleosome arrays; overlapping Di-nucleosome; single-molecule
    DOI:  https://doi.org/10.1016/j.molcel.2025.06.018
  6. Nat Genet. 2025 Jul 21.
    NKX2-1 drives neuroendocrine transdifferentiation of prostate cancer via epigenetic and 3D chromatin remodeling.
    Xiaodong Lu, Viriya Keo, Irina Cheng, Wanqing Xie, Galina Gritsina, Juan Wang, Lina Lu, Cheng-Kai Shiau, Yueying He, Qiushi Jin, Peng Jin, Martin G Sanda, Victor G Corces, Nicolas Altemose, Ruli Gao, Jonathan C Zhao, Jindan Yu.
      A substantial amount of castration-resistant prostate cancer (CRPC) progresses into a neuroendocrine (NE) subtype, known as NEPC, which is associated with poor clinical outcomes. Here we report distinct three-dimensional chromatin architectures between NEPC and CRPC tumors, which were recapitulated by isogenic cell lines undergoing NE transformation (NET). Mechanistically, pioneer factors such as FOXA2 initiate binding at NE enhancers to mediate regional DNA demethylation and induce neural transcription factor (TF) NKX2-1 expression. NKX2-1 preferentially binds gene promoters and interacts with enhancer-bound FOXA2 through chromatin looping. NKX2-1 is highly expressed in NEPC and indispensable for NET of prostate cancer. NKX2-1/FOXA2 further recruits p300/CBP to activate NE enhancers, and pharmacological inhibition of p300/CBP effectively blunts NE gene expression and abolishes NEPC tumor growth. Taken together, our study reports a hierarchical network of TFs governed by NKX2-1 in critically regulating chromatin remodeling and driving luminal-to-NE transformation and suggests promising therapeutic approaches to mitigate NEPC.
    DOI:  https://doi.org/10.1038/s41588-025-02265-4
  7. Nucleic Acids Res. 2025 Jul 19. pii: gkaf671. [Epub ahead of print]53(14):
    SMAdd-seq: probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing.
    Gali Bai, Namrita Dhillon, Colette Felton, Brett Meissner, Brandon Saint-John, Robert Shelansky, Elliot Meyerson, Eva Hrabeta-Robinson, Babak Hodjat, Hinrich Boeger, Angela N Brooks.
      Studies of in vivo chromatin organization have relied on the accessibility of the underlying DNA to nucleases or methyltransferases, which is limited by their requirement for purified nuclei and enzymatic treatment. Here, we introduce a nanopore-based sequencing technique called small-molecule adduct sequencing (SMAdd-seq), where we profile chromatin accessibility by treating nuclei or intact cells with a small molecule, angelicin. Angelicin preferentially forms photoadducts with thymine bases in linker DNA, thereby labeling accessible DNA regions. By applying SMAdd-seq in Saccharomyces cerevisiae, we demonstrate that angelicin-modified DNA can be detected by its distinct nanopore current signals. To systematically identify angelicin modifications and analyze chromatin structure, we developed a neural network model, NEural network for mapping MOdifications in nanopore long-reads (NEMO). NEMO accurately called expected nucleosome occupancy patterns near transcription start sites at both bulk and single-molecule levels. We observe heterogeneity in chromatin structure and identify clusters of single-molecule reads with varying configurations at specific yeast loci. Furthermore, SMAdd-seq performs equivalently on purified yeast nuclei and intact cells, indicating the promise of this method for in vivo chromatin labeling on long single molecules to measure native chromatin dynamics and heterogeneity.
    DOI:  https://doi.org/10.1093/nar/gkaf671
  8. Nat Commun. 2025 Jul 23. 16(1): 6766
    Dissecting the enhancer gene regulatory network in early Drosophila spermatogenesis.
    Patrick van Nierop Y Sanchez, Pallavi Santhi Sekhar, Kerem Yildirim, Tim Lange, Laura Zoe Kreplin, Vigneshwarr Muruga Boopathy, Stephanie Rosswag de Souza, Kim Dammer, David Ibberson, Qian Wang, Katrin Domsch, Anniek Stokkermans, Shubhanshu Pandey, Petra Kaspar, Rafael Martinez-Gallegos, Xuefan Gao, Aakriti Singh, Natalja Engel, Fillip Port, Michael Boutros, Josephine Bageritz, Ingrid Lohmann.
      Cellular decision-making and tissue homeostasis are governed by transcriptional networks shaped by chromatin accessibility. Using single-nucleus multi-omics, we jointly profile gene expression and chromatin accessibility in 10,335 cells from the Drosophila testis apical tip. This enables inference of 147 cell type-specific enhancer-gene regulons using SCENIC + . We functionally validate key transcription factors, including ovo and klumpfuss, known from other stem cell systems but not previously linked to spermatogenesis. CRISPR-mediated knockout reveals their essential roles in germline stem cell regulation, and we provide evidence that they co-regulate shared targets through overlapping enhancer elements. We further uncover a critical role for canonical Wnt signaling, with Pangolin/Tcf activating lineage-specific targets in the germline, soma, and niche. The Pan eRegulon links Wnt activity to cell adhesion, intercellular signaling and germline stem cell maintenance. Together, our study defines the enhancer-driven regulatory landscape of early spermatogenesis and reveals conserved, combinatorial mechanisms of niche-dependent stem cell control.
    DOI:  https://doi.org/10.1038/s41467-025-62046-9
  9. Nat Cell Biol. 2025 Jul 22.
    The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate.
    Harold C Marin, Charlie Allen, Eric Simental, Eric W Martin, Barbara Panning, Bassem Al-Sady, Abigail Buchwalter.
      Heterochromatic loci marked by histone H3 lysine 9 dimethylation (H3K9me2) are enriched at the nuclear periphery in metazoans, but the effect of spatial position on heterochromatin function has not been defined. Here we remove three nuclear lamins and the lamin B receptor (LBR) in mouse embryonic stem cells and show that heterochromatin detaches from the nuclear periphery. Mutant mouse embryonic stem cells sustain naive pluripotency and maintain H3K9me2 across the genome but cannot repress H3K9me2-marked genes or transposons. Further, mutant cells fail to differentiate into epiblast-like cells, a transition that requires the expansion of H3K9me2 across the genome. Mutant epiblast-like cells can silence naive pluripotency genes and activate epiblast-stage genes. However, H3K9me2 cannot repress markers of alternative fates, including primitive endoderm. We conclude that the lamins and LBR control the spatial position, dynamic remodelling and repressive capacity of H3K9me2-marked heterochromatin to shape cell fate decisions.
    DOI:  https://doi.org/10.1038/s41556-025-01703-z
  10. Genome Biol. 2025 Jul 23. 26(1): 219
    Joint representation and visualization of derailed cell states with Decipher.
    Achille Nazaret, Joy Linyue Fan, Vincent-Philippe Lavallée, Cassandra Burdziak, Andrew E Cornish, Vaidotas Kiseliovas, Robert L Bowman, Ignas Masilionis, Jaeyoung Chun, Shira E Eisman, James Wang, Justin Hong, Lingting Shi, Ross L Levine, Linas Mazutis, David Blei, Dana Pe'er, Elham Azizi.
      Biological insights often depend on comparing conditions such as disease and health. Yet, we lack effective computational tools for integrating single-cell genomics data across conditions or characterizing transitions from normal to deviant cell states. Here, we present Decipher, a deep generative model that characterizes derailed cell-state trajectories. Decipher jointly models and visualizes gene expression and cell state from normal and perturbed single-cell RNA-seq data, revealing shared and disrupted dynamics. We demonstrate its superior performance across diverse contexts, including in pancreatitis with oncogene mutation, acute myeloid leukemia, and gastric cancer.
    Keywords:  Acute myeloid leukemia; Cell-state trajectories; Deep generative model; Dimensionality reduction
    DOI:  https://doi.org/10.1186/s13059-025-03682-8
  11. Nucleic Acids Res. 2025 Jul 19. pii: gkaf684. [Epub ahead of print]53(14):
    Spatial-scERA: a method for reconstructing spatial single-cell enhancer activity in multicellular organisms.
    Baptiste Alberti, Séverine Vincent, Isabelle Stévant, Damien Lajoignie, Hélène Tarayre, Juliette Mendes, Sergio Sarnataro, Paul Villoutreix, Yad Ghavi-Helm.
      Enhancers play an essential role in developmental processes by regulating the spatiotemporal expression of genes. Characterizing their spatiotemporal activity remains however an important challenge. Here we introduce a novel in vivo/in silico method for spatial single-cell enhancer-reporter assays (spatial-scERA) designed to reconstruct the spatial activity of candidate enhancer regions in parallel in multicellular organisms. Spatial-scERA integrates parallel reporter assays with single-cell RNA sequencing and spatial reconstruction using optimal transport, to map cell-type-specific enhancer activity at the single-cell level on a 3D virtual sample. We evaluated spatial-scERA in Drosophila embryos using 25 candidate enhancers, and validated the robustness of our reconstructions by comparing them to in situ hybridization. Remarkably, spatial-scERA faithfully reconstructed the spatial activity of these enhancers, even when the reporter construct was expressed in as few as 10 cells. Our results demonstrate the importance of integrating transcriptomic and spatial data for accurately predicting enhancer activity patterns in complex multicellular samples and linking enhancers to their potential target genes. Overall, spatial-scERA provides a scalable approach to map the spatial activity of enhancers at single-cell resolution without the need for imaging or a priori knowledge of embryology and can be applied to any multicellular organism amenable to transgenesis.
    DOI:  https://doi.org/10.1093/nar/gkaf684
  12. Cell Rep. 2025 Jul 18. pii: S2211-1247(25)00781-8. [Epub ahead of print] 116010
    A STAT3/integrin axis accelerates pancreatic cancer initiation and progression.
    Alejandro D Campos, Ryan M Shepard, Zachary Ortega, Ingrid Heumann, Anna E Wilke, Arin Nam, Carson Cable, Kourosh Kouhmareh, Richard Klemke, Nicole M Mattson, Trey Ideker, Camila De Arruda Saldanha, Sven Heinz, Valerie Weaver, Tami Von Schalscha, Hiromi I Wettersten, Sara M Weis, David A Cheresh.
      The signal transducer and activator of transcription 3 (STAT3) pathway drives pancreatic ductal adenocarcinoma (PDAC) progression by coordinating cellular responses to stress and inflammation. We perform ChIP-seq on hypoxia- or oncostatin-M-treated PDAC cells to identify sites at which phospho-STAT3 binds to regulate the expression of genes linked to poor survival. A top hit among these is ITGB3, which we show promotes PDAC initiation and progression. Single-cell transcriptomics reveal that ITGB3 expression is enriched in PDAC cells experiencing oxidative stress due to chemotherapy. Moreover, high ITGB3 expression positively correlates with STAT3 signaling, hypoxia, and the basal subtype. Mechanistically, chromatin accessibility at ITGB3 enhancers controls STAT3's ability to induce ITGB3 expression, illuminating a plastic regulatory mechanism modulating STAT3 activity. Leveraging this insight, we identify additional STAT3 target genes regulated similarly to ITGB3 to establish an 18-gene signature involved in adaptive responses and able to stratify survival outcomes. Collectively, these findings highlight a novel opportunity to stratify PDAC subpopulations for STAT3-targeted therapies.
    Keywords:  CP: Cancer; STAT3; cellular stress; cytokine; enhancer; gene signature; hypoxia; inflammation; integrin; pancreatic cancer; tumor initiation
    DOI:  https://doi.org/10.1016/j.celrep.2025.116010
  13. iScience. 2025 Jul 18. 28(7): 112855
    Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte development.
    Johanna Tingvall-Gustafsson, Christina T Jensen, Jonas Ungerbäck, Mikael Sigvardsson.
      Stage- and lineage-specific gene expression patterns are controlled by a complex interplay between transcription factors, the epigenetic landscape, and the three-dimensional (3D) structure of the DNA. The 3D structure allows for the formation of DNA loops that juxtaposition distal regulatory elements to the promoters, allowing for tight control of gene expression. Developing a tool to facilitate the exploration of complex gene regulatory networks based on chromosome configuration data in early lymphocytes, we show that lineage-specific transcription factors target regulatory elements annotated to both lineage-specific and broadly expressed genes. Several regulatory elements annotated to lineage-specific genes were also annotated to alternative promoters in a context-dependent manner, revealing a highly complex interplay between promoters and DREs in early lymphocyte development. These data highlight how efficient annotation procedures for linking distal regulatory elements to target genes provide valuable insights into gene regulatory networks.
    Keywords:  Chromosome organization; Components of the immune system; Epigenetics; Molecular genetics
    DOI:  https://doi.org/10.1016/j.isci.2025.112855
  14. Mol Cell. 2025 Jul 16. pii: S1097-2765(25)00575-1. [Epub ahead of print]
    Structural mechanism of H3K27 demethylation and crosstalk with heterochromatin markers.
    Chien-Chu Lin, Yani Zhao, Caroline A Foley, Aspen T Hawkins, Lindsey I James, Stephen V Frye, Robert K McGinty.
      Histone H3 lysine 27 trimethylation (H3K27me3) is a repressive histone modification that is a hallmark of facultative heterochromatin. H3K27me3 is installed by the polycomb repressive complex 2 (PRC2) and removed by KDM6 family Jumonji C (JmjC) domain demethylases. Structural studies have elucidated how PRC2 functions on nucleosomes and its regulation by local histone modification signatures. However, the molecular mechanisms governing H3K27 demethylation to reactivate silenced chromatin remain poorly understood. Here, we report the cryoelectron microscopy (cryo-EM) structure of mouse KDM6B bound to the nucleosome. Our structure shows how KDM6B engages wrapped nucleosomal DNA together with both extranucleosomal DNA linkers to position its catalytic JmjC domain for H3K27 demethylation. KDM6B induces an overlapped linker DNA conformation consistent with function in a compact chromatin environment. We further show that linker histones and H2AK119ub1, both enriched in heterochromatin, antagonize KDM6B function, suggesting that linker histone eviction and H2A deubiquitylation precede H3K27 demethylation during heterochromatin activation.
    Keywords:  H3K27me3; KDM6B; chromatin; cryo-EM; epigenetics; heterochromatin; histone; lysine demethylase; nucleosome; post-translation modification
    DOI:  https://doi.org/10.1016/j.molcel.2025.06.025
  15. Nat Genet. 2025 Jul 22.
    G-quadruplexes are promoter elements controlling nucleosome exclusion and RNA polymerase II pausing.
    Cyril Esnault, Amal Zine El Aabidine, Marie-Cécile Robert, Anne Cucchiarini, Talha Magat, Alexia Pigeot, Soumya Bouchouika, Encar Garcia-Oliver, Kevin Gawron, Eugénia Basyuk, Magdalena A Karpinska, Alja Kozulic-Pirher, Yu Luo, Daniela Verga, Raphael Mourad, Ovidiu Radulescu, Jean-Louis Mergny, Edouard Bertrand, Jean-Christophe Andrau.
      Despite their central role in transcription, it has been difficult to define universal sequences associated with eukaryotic promoters. Within the chromatin context, recruitment of transcriptional machinery requires promoter opening, but how DNA elements contribute to this process is unclear. Here we show that G-quadruplex (G4) secondary DNA structures are highly enriched at mammalian promoters. G4s are located at the deepest point of nucleosome exclusion at promoters and correlate with maximum promoter activity. We found that experimental G4s exclude nucleosomes in vivo and in vitro while favouring strong positioning. At model promoters, impairing G4s affected both transcriptional activity and chromatin opening. G4 destabilization also resulted in an inactive promoter state and affected the transition to effective RNA production. Finally, G4 stabilization resulted in global reduction of proximal promoter pausing. Altogether, our data introduce G4s as bona fide promoter elements allowing nucleosome exclusion and facilitating pause-release by RNA polymerase II.
    DOI:  https://doi.org/10.1038/s41588-025-02263-6
  16. Science. 2025 Jul 24. eadx3800
    High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer.
    Luke W Koblan, Kathryn E Yost, Pu Zheng, William N Colgan, Matthew G Jones, Dian Yang, Arhan Kumar, Jaspreet Sandhu, Alexandra Schnell, Dawei Sun, Can Ergen, Reuben A Saunders, Xiaowei Zhuang, William E Allen, Nir Yosef, Jonathan S Weissman.
      Charting the spatiotemporal dynamics of cell fate determination in development and disease is a long-standing objective in biology. Here we present the design, development, and extensive validation of PEtracer, a prime editing-based, evolving lineage tracing technology compatible with both single-cell sequencing and multimodal imaging methodologies to jointly profile cell state and lineage in dissociated cells or while preserving cellular context in tissues with high spatial resolution. Using PEtracer coupled with MERFISH spatial transcriptomic profiling in a syngeneic mouse model of tumor metastasis, we reconstruct the growth of individually-seeded tumors in vivo and uncover distinct modules of cell-intrinsic and cell-extrinsic factors that coordinate tumor growth. More generally, PEtracer enables systematic characterization of cell state and lineage relationships in intact tissues over biologically-relevant temporal and spatial scales.
    DOI:  https://doi.org/10.1126/science.adx3800
  17. Nat Commun. 2025 Jul 21. 16(1): 6677
    E2F activity determines mitosis versus whole-genome duplication in G2-arrested cells.
    Kibum Kim, Jessica Armand, Sungsoo Kim, Hee Won Yang.
      While mitogenic signaling is known to regulate cell-cycle entry during the G1 phase, its function in the G2 phase remains elusive. Here we show that mitogenic signaling controls whether G2-arrested cells proceed through mitosis or undergo whole-genome duplication. Although mitogenic signaling is not required for the G2/M transition under normal conditions, it modulates E2F transcriptional activity via c-Myc. When G2 arrest occurs due to CDK4/6 and CDK2 suppression, E2F activity levels determine the status of APC/C inactivation and the CDK2-Rb feedback loop. Upon release from G2 arrest, cells maintaining APC/C inactivation promptly induce CDK2 activation and FoxM1 phosphorylation, driving mitotic entry. Conversely, APC/C reactivation degrades cyclin A and abolishes the CDK2-Rb loop, necessitating CDK4/6 activation for cell-cycle re-entry. This regulatory mechanism mirrors the G1-phase process, resulting in whole-genome duplication. In cancer cells, this process promotes genome instability and oncogene amplification, contributing to aggressive behavior. These findings reveal a previously unrecognized mitogen-dependent checkpoint that governs cell fate in the G2 phase.
    DOI:  https://doi.org/10.1038/s41467-025-62061-w
  18. Nat Commun. 2025 Jul 19. 16(1): 6662
    The invasion phenotypes of glioblastoma depend on plastic and reprogrammable cell states.
    Milena Doroszko, Rebecka Stockgard, Irem Uppman, Josephine Heinold, Faidra Voukelatou, Hitesh Bhagavanbhai Mangukiya, Thomas O Millner, Madeleine Skeppås, Mar Ballester Bravo, Ramy Elgendy, Maria Berglund, Ludmila Elfineh, Cecilia Krona, Soumi Kundu, Katarzyna Koltowska, Silvia Marino, Ida Larsson, Sven Nelander.
      Glioblastoma (GBM) is the most common primary brain cancer. It causes death mainly by local invasion via several routes, including infiltration of white matter tracts and penetration of perivascular spaces. However, the pathways that mediate these invasion routes are only partly known. Here, we conduct an integrative study to identify cell states and central drivers of route-specific invasion in GBM. Combining single-cell profiling and spatial protein detection in patient-derived xenograft models and clinical tumor samples, we demonstrate a close association between the differentiation state of GBM cells and their choice of invasion route. Computational modeling identifies ANXA1 as a driver of perivascular involvement in GBM cells with mesenchymal differentiation and the transcription factors RFX4 and HOPX as orchestrators of growth and differentiation in diffusely invading GBM cells. Ablation of these targets in tumor cells alters their invasion route, redistributes the cell states, and extends survival in xenografted mice. Our results define a close association between GBM cell differentiation states and invasion routes, identify functional biomarkers of route-specific invasion, and point toward targeted modulation of specific invasive cell states as a therapeutic strategy in GBM.
    DOI:  https://doi.org/10.1038/s41467-025-61999-1
  19. Nat Biotechnol. 2025 Jul 22.
    Combined single-cell profiling of chromatin-transcriptome and splicing across brain cell types, regions and disease state.
    Wen Hu, Careen Foord, Justine Hsu, Li Fan, Michael J Corley, Samantha N Lanjewar, Siwei Xu, Natan Belchikov, Yi He, Alina P S Pang, Tarun N Bhatia, Julien Jarroux, Anoushka Joglekar, Teresa A Milner, Lishomwa C Ndhlovu, Jing Zhang, Eduardo Butelman, Steven A Sloan, Virginia M Y Lee, Li Gan, Hagen U Tilgner.
      Measuring splicing and chromatin accessibility simultaneously in frozen tissues remains challenging. Here we combined single-cell isoform RNA sequencing and assay for transposase accessible chromatin (ScISOr-ATAC) to interrogate the correlation between these modalities in single cells in human and rhesus macaque frozen cortical tissue samples. Applying a previous definition of four 'cell states' in which the transcriptome and chromatin accessibility are coupled or decoupled for each gene, we demonstrate that splicing patterns in one cell state can differ from those of another state within the same cell type. We also use ScISOr-ATAC to measure the correlation of chromatin and splicing across brain cell types, cortical regions and species (macaque and human) and in Alzheimer's disease. In macaques, some excitatory neuron subtypes show brain-region-specific splicing and chromatin accessibility. In human and macaque prefrontal cortex, strong evolutionary divergence in one molecular modality does not necessarily imply strong divergence in another modality. Finally, in Alzheimer's disease, oligodendrocytes show high dysregulation in both chromatin and splicing.
    DOI:  https://doi.org/10.1038/s41587-025-02734-5
  20. Nucleic Acids Res. 2025 Jul 19. pii: gkaf669. [Epub ahead of print]53(14):
    PPARG-centric transcriptional re-wiring during differentiation of human trophoblast stem cells into extravillous trophoblasts.
    Qingqing Guo, Joonhyuk Choi, Muyoung Lee, Jonghwan Kim.
      Peroxisome proliferator-activated receptor gamma (PPARG) is a nuclear receptor family transcription factor (TF) critical for adipogenesis, lipid metabolism, insulin sensitivity, and inflammation. It has also been known to play essential roles in trophoblast development and placentation. Dysregulation of PPARG in trophoblast differentiation has been implicated in pregnancy complications, such as pre-eclampsia and gestational diabetes. However, the molecular mechanisms of PPARG-dependent target gene regulation and its interactions with other regulatory factors during human trophoblast differentiation remain unclear. Using human trophoblast stem cells (TSCs), mimicking placental cytotrophoblasts (CTs), and their differentiation into extravillous trophoblasts (EVTs) as our models, we reveal that PPARG has cell-type-specific targets in TSCs and EVTs. We also find that while PPARG is essential for both TSC self-renewal and EVT differentiation, only its role in EVT differentiation is ligand sensitive and requires ligand-binding domain (LBD)-mediated transcriptional activity, whereas its function in TSC self-renewal appears to be ligand insensitive. Combined analysis with chromosomal targets of previously defined key TFs in TSCs and EVTs shows that PPARG forms trophoblast cell-type-specific regulatory circuitries, leading to differential target gene regulation via transcriptional re-wiring during EVT differentiation. Additionally, the enhanced invasiveness of EVTs treated with a PPARG agonist suggests a potential connection between PPARG pathways and human placenta accreta.
    DOI:  https://doi.org/10.1093/nar/gkaf669
  21. Nat Commun. 2025 Jul 23. 16(1): 6803
    The histone H3 lysine 36 demethylase KDM2A/FBXL11 controls Polycomb-mediated gene repression and germ cell development in male mice.
    Michael T Bocker, Grigorios Fanourgakis, Kristie Wetzel, Pavel A Komarov, Hélène Royo, Alexia Rohmer, Sunwoo Chun, Ching-Yeu Liang, Hubertus Kohler, Taiping Chen, Xiaohong Mao, Mark A Labow, Reginald A Valdez, Michael B Stadler, Dirk G de Rooij, Paola Capodieci, John Tallarico, Antoine H F M Peters, Thomas B Nicholson.
      KDM2A/FBXL11 is a Jumonji-domain containing lysine demethylase catalyzing the removal of mono- and di-methyl modifications of histone H3 lysine 36 (H3K36me1/2). While Kdm2a is required for mouse embryogenesis, its role in adult physiology has been largely unexplored. Using conditional deletion approaches, we demonstrate that Kdm2a deficiency leads to testicular atrophy and male infertility. Although spermatogonial stem cells remain unaffected, proliferating and differentiating spermatogonia exhibit delayed cell cycle progression and apoptosis. RNA-sequencing of purified spermatogonia and spermatocytes reveals Kdm2a-dependent repression of over 750 genes during spermatogonial differentiation. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) demonstrates increased H3K36me2 levels at CpG-rich gene promoters in Kdm2a-deficient spermatogonia. KDM2A is required for Polycomb-mediated repression as shown by increased H3K36me2 and reduced H3K27me3 promoter occupancies and failed gene repression in Kdm2a deficient differentiating spermatogonia. Loss of Kdm2a in spermatocytes disrupts progression through meiotic prophase, as evidenced by impaired completion of chromosome synapsis and processing of meiotic double-strand breaks (DSBs), by altered chromatin states and by an impairment of X-linked gene repression. Our study thus identifies critical roles for KDM2A in coordinating gene expression programs during spermatogonial differentiation and meiosis, which are essential for male germ cell development.
    DOI:  https://doi.org/10.1038/s41467-025-61733-x
  22. Mol Cell. 2025 Jul 15. pii: S1097-2765(25)00578-7. [Epub ahead of print]
    Single-molecule live imaging of subunit interactions and exchange within cellular regulatory complexes.
    Thomas G W Graham, Claire Dugast-Darzacq, Gina M Dailey, Britney Weng, Sathvik Anantakrishnan, Xavier Darzacq, Robert Tjian.
      Cells are built from vast networks of interdependent molecular interactions. Here, we combine proximity-assisted photoactivation (PAPA) with automated fast single-molecule tracking (fSMT) to probe subunit interactions within endogenous protein complexes in live human cells. PAPA-fSMT revealed that the inactive positive transcription elongation factor b (P-TEFb):7SK ribonucleoprotein complex is predominantly mobile, not tethered to chromatin, and detected interaction of specific heterogeneous nuclear ribonucleoproteins (hnRNPs) with the 7SK complex. Cyclin-dependent kinase 9 (Cdk9) inhibition liberated hnRNP R from large RNAs, increased hnRNP R binding to 7SK, and evicted P-TEFb from 7SK within minutes-consistent with rapid, homeostatic negative feedback regulation of P-TEFb by competing protein-RNA interactions. Association with the coactivator BRD4 increased P-TEFb chromatin binding, which depended on the BRD4 bromodomains. Finally, PAPA detected the release of P-TEFb from 7SK by the HIV transcriptional activator Tat. Our results illuminate aspects of P-TEFb regulation that were previously inaccessible in live cells and open a route to probe subunit interactions and exchange within endogenous regulatory complexes.
    Keywords:  7SK complex; BRD4; HIV Tat; P-TEFb; PAPA; fSMT; fast single-molecule tracking; heterogeneous nuclear ribonucleoproteins; hnRNP R; hnRNPs; positive transcription elongation factor b; protein-protein interactions; proximity-assisted photoactivation; transcriptional regulation
    DOI:  https://doi.org/10.1016/j.molcel.2025.06.028
  23. Proc Natl Acad Sci U S A. 2025 Jul 29. 122(30): e2425319122
    Leveraging chromatin packing domains to target chemoevasion in vivo.
    Jane Frederick, Ranya K A Virk, I Chae Ye, Luay M Almassalha, Greta M Wodarcyk, David VanDerway, Ruyi Gong, Cody L Dunton, Tiffany Kuo, Karla I Medina, Margarita Loxas, Jared T Ahrendsen, Demirkan B Gursel, Paola Carrillo Gonzalez, Rikkert J Nap, Saira John, Vasundhara Agrawal, Nicholas M Anthony, John Carinato, Wing Shun Li, Rivaan Kakkaramadam, Surbhi Jain, Shohreh Shahabi, Guillermo A Ameer, Igal G Szleifer, Vadim Backman.
      Cancer cells exhibit a remarkable resilience to cytotoxic stress, often adapting through transcriptional changes linked to alterations in chromatin structure. In several types of cancer, these adaptations involve epigenetic modifications and restructuring of topologically associating domains. However, the underlying principles by which chromatin architecture facilitates such adaptability across different cancers remain poorly understood. To investigate the role of chromatin in this process, we developed a physics-based model that connects chromatin organization to cell fate decisions, such as survival following chemotherapy. Our model builds on the observation that chromatin forms packing domains, which influence transcriptional activity through macromolecular crowding. The model accurately predicts chemoevasion in vitro, suggesting that changes in packing domains affect the likelihood of survival. Consistent results across diverse cancer types indicate that the model captures fundamental principles of chromatin-mediated adaptation, independent of the specific cancer or chemotherapy mechanisms involved. Based on these insights, we hypothesized that compounds capable of modulating packing domains, termed Transcriptional Plasticity Regulators (TPRs), could prevent cellular adaptation to chemotherapy. We conducted a proof-of-concept compound screen using live-cell chromatin imaging to identify several TPRs that synergistically enhanced chemotherapy-induced cell death. The most effective TPR significantly improved therapeutic outcomes in a patient-derived xenograft model of ovarian cancer. These findings underscore the central role of chromatin in cellular adaptation to cytotoxic stress and present a framework for enhancing cancer therapies, with broad potential across multiple cancer types.
    Keywords:  Biophysics; cancer; chemotherapy; chromatin; plasticity
    DOI:  https://doi.org/10.1073/pnas.2425319122
  24. Genome Biol. 2025 Jul 24. 26(1): 220
    Modeling combinatorial regulation from single-cell multi-omics provides regulatory units underpinning cell type landscape using cRegulon.
    Zhanying Feng, Xi Chen, Zhana Duren, Jingxue Xin, Hao Miao, Qiuyue Yuan, Yong Wang, Wing Hung Wong.
      Advances in single-cell technology enable large-scale generation of omics data, promising for clarifying gene regulatory networks governing different cell type/states. Nonetheless, prevailing methods fail to account for universal and reusable regulatory modules in GRNs, which are fundamental underpinnings of cell type landscape. We introduce cRegulon to infer regulatory modules by modeling combinatorial regulation of transcription factors based on diverse GRNs from single-cell multi-omics data. Through benchmarking and applications using simulated datasets and real datasets, cRegulon outperforms existing approaches in identifying TF combinatorial modules as regulatory units and annotating cell types. cRegulon offers new insights and methodology into combinatorial regulation.
    DOI:  https://doi.org/10.1186/s13059-025-03680-w
  25. Nucleic Acids Res. 2025 Jul 19. pii: gkaf683. [Epub ahead of print]53(14):
    A phage transcription factor displaces the host σ factor and stabilizes its own σ factor.
    Liqiao Xu, Liang Liang, Linggang Yuan, Yue Yao, Xiaoting Hua, Yu Feng.
      Phages are the most abundant self-replicating entities on earth, and understanding their transcriptional regulation can provide insights into bacterial gene expression mechanisms. The bacterial RNA polymerase core enzyme interacts with various σ factors to recognize and unwind promoter DNA. Gp79, a protein from Escherichia coli phage phiEco32, inhibits host σ70-mediated transcription while simultaneously activating transcription through its own σ factor, gp36. The underlying mechanism of this unusual dual regulatory role has remained unclear. In this study, we present cryo-EM structures of E. coli RNA polymerase (RNAP) in complex with gp79, and of RNAP in complex with gp79, gp36, and a cognate promoter. Structural and biochemical analyses reveal the basis for σ displacement by gp79 and promoter recognition by gp36. Our findings show that the N-terminus of gp79 invades the RNA channel, effectively displacing σ4. Upon encountering gp36, the N-terminus of gp79 adopts a new conformation, binds to gp36, and stabilizes the RNAP-promoter open complex. These findings advance our understanding of phage transcriptional regulation and suggest potential applications for synthetic biology.
    DOI:  https://doi.org/10.1093/nar/gkaf683
  26. Nat Commun. 2025 Jul 18. 16(1): 6629
    Deciphering direct transcriptional effects of epigenetic compounds through large-scale new RNA profiling.
    Leonard Hartmanis, Daniel Ramsköld, Gert-Jan Hendriks, Per Johnsson, Gustav Hallén, Ran Ma, Anton J M Larsson, Salomé Hahne, Christoph Ziegenhain, Johan Hartman, Rickard Sandberg.
      Examining direct transcriptional effects of genetic and chemical perturbations is crucial for understanding gene expression mechanisms. Standard RNA-seq experiments often overlook these direct effects, and current methods for profiling nascent RNA are usually time-consuming. Here, we adapted single-cell 4sU-based sequencing into a scalable, automated mini-bulk format to profile new RNA in smaller cell populations. This approach enabled us to map the direct transcriptional effects of epigenetic regulators. Brief exposure to SAHA (an HDAC inhibitor) revealed hundreds of directly responsive genes, many showing altered transcriptional bursting kinetics, with promoter regions enriched in binding sites for factors including bromodomain proteins. Profiling 83 epigenetic compounds uncovered direct transcriptional impacts from inhibitors of bromodomain proteins, histone deacetylases, and histone demethylases. Notably, chemically similar HDAC inhibitors elicited concordant direct responses and intronic expression analyses mirrored the direct effects seen in new RNA. This work highlights powerful approaches for investigating transcriptional mechanisms.
    DOI:  https://doi.org/10.1038/s41467-025-61769-z
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