bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2025–10–05
eleven papers selected by
Connor Rogerson, University of Cambridge
  1. Genome organization by SATB1 binding to base-unpairing regions (BURs) provides a scaffold for SATB1-regulated gene expression.
  2. ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes.
  3. Long-read nucleosome mapping of single chromatin fibers using DNA methylation and Nanopore sequencing.
  4. ARID1A regulates histone octamer transfer activity of human canonical BAF complex.
  5. A chemical epigenetic tool to probe site-specific DNA-binding protein complexes.
  6. Cell-type-specific functionality encoded within the intrinsically disordered regions of OCT4.
  7. Phase-separated NDF-FACT condensates facilitate transcription elongation on chromatin.
  8. Design principles of transcription factors with intrinsically disordered regions.
  9. Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq.
  10. A needed nomenclature for nucleosomes.
  11. Single-cell nascent transcription reveals sparse genome usage and plasticity.
  1. Elife. 2025 Oct 02. pii: RP105915. [Epub ahead of print]14
    Genome organization by SATB1 binding to base-unpairing regions (BURs) provides a scaffold for SATB1-regulated gene expression.
    Yoshinori Kohwi, Xianrong Wong, Mari Grange, Thomas Sexton, Hunter W Richards, Yohko Kitagawa, Shimon Sakaguchi, Ya-Chen Liang, Cheng-Ming Chuong, Vladimir A Botchkarev, Ichiro Taniuchi, Karen L Reddy, Terumi Kohwi-Shigematsu.
      Mammalian genomes are organized by multi-level folding; yet how this organization contributes to cell-type-specific transcription remains unclear. SATB1 forms a nuclear substructure that resists high-salt extraction. SATB1 binds base-unpairing regions (BURs), genomic elements with high unwinding propensities. In mouse thymocytes, we found that SATB1 establishes a two-tiered chromatin organization: one through indirect binding to transcriptionally active DNase 1-accessible chromatin and another by direct binding to BURs in the DNase 1-inaccessible nuclear substructure. Recently published ChIP-seq datasets show SATB1 binding to accessible chromatin at enhancers and CTCF sites, but not to BURs. By employing urea ChIP-seq, which retains only directly bound protein:DNA complexes, we found that BURs, but not CTCF sites, are direct SATB1 binding targets genome-wide. BURs bound to the SATB1 nuclear substructure interact with accessible chromatin, crossing multiple topologically associated domains (TADs). SATB1 is required for these megabase-scale interactions linked to cell-type-specific gene expression. BURs are highly enriched within transcriptionally repressive lamina-associated domains (LADs). Besides these BURs, SATB1 anchors some BURs (18%) outside LADs near genes in otherwise accessible chromatin to the SATB1 nuclear substructure. Only a subset of total BURs is bound to SATB1, depending on cell type. Notably, despite the mutually exclusive SATB1-binding profiles uncovered by the two ChIP-seq methods, we found most peaks in both profiles are valid and require SATB1. Based on these and previous data, we propose that the SATB1 protein network forms a chromatin scaffold, providing an interface that connects accessible chromatin to a subnuclear architectural structure, thereby facilitating the three-dimensional organization linked to cell-type-specific gene expression.
    Keywords:  SATB1; base-unpairing region; chromatin organization; chromosomes; gene expression; lamina-associated domains; mouse; urea ChIP-seq
    DOI:  https://doi.org/10.7554/eLife.105915
  2. Science. 2025 Oct 02. 390(6768): eadr0018
    ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes.
    Camille Moore, Emily Wong, Upneet Kaur, Un Seng Chio, Ziling Zhou, Megan Ostrowski, Ke Wu, Iryna Irkliyenko, Sean Wang, Vijay Ramani, Geeta J Narlikar.
      Adenosine triphosphate (ATP)-dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remodelers, ACF and RSC, using chromatin condensates and single-molecule footprinting. We find that both remodelers inhibit the formation of condensed chromatin. However, the remodelers have distinct effects on preformed chromatin condensates. ACF spaces nucleosomes without decondensing the chromatin, explaining how ACF maintains nucleosome organization in transcriptionally repressed genomic regions. By contrast, RSC catalyzes ATP-dependent decondensation of chromatin. RSC also drives micron-scale movements of entire chromatin condensates. These additional activities of RSC may contribute to its central role in transcription. The biological importance of remodelers may thus reflect both their effects on nucleosome mobilization and the corresponding consequences on chromatin dynamics at the mesoscale.
    DOI:  https://doi.org/10.1126/science.adr0018
  3. Biophys J. 2025 Oct 01. pii: S0006-3495(25)00648-4. [Epub ahead of print]
    Long-read nucleosome mapping of single chromatin fibers using DNA methylation and Nanopore sequencing.
    Gert-Jan Kuijntjes, Tineke L Lenstra, John van Noort.
      DNA elements such as genes and their regulatory regions must become accessible for protein binding when transcription is activated, which requires reorganization of the nucleosomes that fold the DNA into chromatin fibers. MNase-seq has been instrumental in uncovering the interplay between gene activity and chromatin organization by mapping the average nucleosome occupancy in populations of cells. However, better mechanistic understanding can be obtained from assays that can map nucleosomes along long strands of DNA at single-molecule resolution and without averaging. Here, we show that the combination of DNA methylation, long-read Nanopore sequencing and a novel nucleosome mapping algorithm based on statistical physics results in precise nucleosome footprinting at the single-molecule level over DNA loci exceeding several 10s of kbp. Accurate nucleosome mapping was verified in vitro, using chromatin reconstituted on tandem arrays of nucleosome positioning elements. Genome-wide application on Saccharomyces cerevisiae grown in different transcriptional conditions revealed large heterogeneity of nucleosome distributions upon transcription activation of the model GAL locus. Moreover, neighboring repeats of the ribosomal transcript RDN1 featured long-range correlations in nucleosome occupancy that we attribute to differential transcriptional activity. This enhanced assay allows for both meta-occupancy analysis, as well as in-depth single-fiber comparisons of local chromatin aberrations in context of transcription, DNA repair and other processes, illustrating the added value of single-molecule nucleosome mapping using long-read sequencing compared to traditional population averaged maps.
    DOI:  https://doi.org/10.1016/j.bpj.2025.09.048
  4. Nucleic Acids Res. 2025 Sep 23. pii: gkaf958. [Epub ahead of print]53(18):
    ARID1A regulates histone octamer transfer activity of human canonical BAF complex.
    Naoe Moro, Yukiko Fujisawa-Tanaka, Shinya Watanabe.
      Mutations that impact subunits of mammalian SWI/SNF (mSWI/SNF or BAF) chromatin remodeling complexes are found in over 20% of human cancers. Among these subunits, AT-rich interactive domain-containing protein 1A (ARID1A) is the most frequently mutated gene, occurring in over 8% of various cancers. The majority of ARID1A mutations are frameshift or nonsense mutations, causing loss of function. Previous studies have suggested that ARID1A may facilitate interactions between BAF complexes and various transcriptional coactivators, but a biochemical role for ARID1A in BAF remodeling activity has not been identified. Here, we describe the in vitro reconstitution of the cBAF, PBAF, and ncBAF complexes, and we compare their biochemical activities. In addition, we reconstitute a variety of cBAF subcomplexes, defining roles for several subunits in high affinity nucleosome binding and nucleosome sliding activity. Remarkably, we find that the ARID1A subunit of cBAF is largely dispensable for nucleosome binding, nucleosome sliding, and adenosine triphosphatase activity, but ARID1A is required for cBAF to transfer histone octamers between DNA templates. Our study reveals a biochemical function of ARID1A/ARID1B in BAF-mediated chromatin remodeling, suggesting a model in which dysregulation of histone octamer transfer activity of BAF complexes may be relevant to cancer formation.
    DOI:  https://doi.org/10.1093/nar/gkaf958
  5. Proc Natl Acad Sci U S A. 2025 Oct 07. 122(40): e2509021122
    A chemical epigenetic tool to probe site-specific DNA-binding protein complexes.
    Jiajun Zhu, Zhucui Li, Dongxiang Xue, Zihe Meng, Sida Shao, Julian Pulecio, Guoan Zhang, Danwei Huangfu, Todd Evans, Shuibing Chen, Peter G Schultz.
      Site-specific DNA binding by proteins is critical for regulating transcriptional activity and cell fate decision. However, identifying proteins bound to specific genomic regions (e.g., promoter or enhancer regions) remains challenging. To address this, we developed a chemical epigenetic tool, named Site-specific noncanonical amino acid-mediated capture of protein (SCOPE), incorporating a photo-crosslinking amino acid into a nuclease-deficient dCas9 mutant. Human pluripotent stem cells (hPSCs) carrying SCOPE enable the capture of proteins bound to, in theory, any genomic location, facilitating the study of the cell context-dependent DNA-protein interactions. Using SCOPE, we identified the OCT4/SOX2/CARHSP1 complex binding to the NANOG promoter to maintain pluripotency in hPSCs. During ectoderm differentiation, ZIC2 acts as a competitive inhibitor, binding the same promoter region to downregulate NANOG expression and promote differentiation. Additionally, SCOPE identified that ZNF8 binds to the distal regulatory region of OCT4 to maintain naïve pluripotency. In summary, SCOPE provides a robust system for uncovering cell context-dependent, site-specific genome regulators, offering valuable insights into gene regulation networks driving cell fate transitions.
    Keywords:  NANOG regulators; noncanonical amino acid; photo-crosslink; protein–DNA interactions
    DOI:  https://doi.org/10.1073/pnas.2509021122
  6. Nat Commun. 2025 Sep 30. 16(1): 8647
    Cell-type-specific functionality encoded within the intrinsically disordered regions of OCT4.
    Burak Ozkan, Mitzy Rios de Anda, Elisa Hall-Ponsele, Maria Rosa Portero Migueles, Amani Alshaikh, Marta Hanzevacki, Moriyah Naama, Katharine Furlong, Gareth A Roberts, Meryam Beniazza, My Linh Huynh, Michael R O'Dwyer, Sonia Yiakoumi, Christos Spanos, Hazar Yassen, Keisuke Kaji, Hitoshi Niwa, Yosef Buganim, Sally Lowell, Abdenour Soufi.
      The cell-type-specific function of transcription factors (TFs) is crucial for determining cellular identity. However, it is unclear how a single TF can function specifically in different cell types. Here, we define the molecular features that enable OCT4 to reprogram somatic cells into pluripotent or trophoblast stem cells, maintain the self-renewal of embryonic stem cells (ESCs), and drive lineage commitment during early embryonic development. Embedded within the intrinsically disordered regions (IDRs) of OCT4, we uncover short linear peptides that are essential for reprogramming (SLiPERs) but dispensable for ESC self-renewal. SLiPERs adopt a quasi-ordered state and, during reprogramming, recruit a unique set of proteins to closed chromatin that are unnecessary for ESC self-renewal. Interestingly, SLiPERs are essential for embryos to develop beyond late gastrulation. Removing SLiPERs leads to aberrant OCT4 binding, derailing the regular transition of ESCs out of pluripotency. Our findings identify modules within IDRs that contribute to the functional versatility and specificity of TFs.
    DOI:  https://doi.org/10.1038/s41467-025-63806-3
  7. Nat Cell Biol. 2025 Sep 30.
    Phase-separated NDF-FACT condensates facilitate transcription elongation on chromatin.
    Ziwei Li, Francesca Burgos-Bravo, Kevin Xu, Chen Li, Kelvin Y Kwan, Alexander B Tong, Zelin Shan, Huan Wang, Motoki Takaku, Joey Li, Zheng Shi, Dmitry Lyumkis, Carlos Bustamante, Jia Fei.
      How the facilitates chromatin transcription (FACT) complex enables RNA polymerase II to overcome chromatin barriers in cells remains poorly understood-especially given the limited direct interactions of FACT with polymerases, DNA or nucleosomes. Here we demonstrate that phase separation, mediated by nucleosome destabilizing factor (NDF), is a key mechanism enabling the function of FACT during transcription elongation. Through biochemical and single-molecule assays, we found that NDF-FACT condensates create specialized biochemical environments that enhance transcription efficiency approximately 20-fold compared with FACT alone. These dynamic condensates form on transcribing RNA polymerase II and travel along chromatin, where they promote efficient nucleosome disassembly at barriers while retaining histones on DNA to preserve chromatin integrity. In human stem cells, disruption of these condensates leads to genome-wide transcriptional defects and chromatin instability, mirroring the effects of FACT depletion. By showing that phase separation enhances FACT function during transcription elongation, our study reveals a key mechanism that preserves chromatin integrity and transcriptional homeostasis in human stem cells.
    DOI:  https://doi.org/10.1038/s41556-025-01778-8
  8. Elife. 2025 Sep 30. pii: RP104956. [Epub ahead of print]14
    Design principles of transcription factors with intrinsically disordered regions.
    Wencheng Ji, Ori Hachmo, Naama Barkai, Ariel Amir.
      Transcription factors (TFs) are proteins crucial for regulating gene expression. Effective regulation requires the TFs to rapidly bind to their correct target, enabling the cell to respond efficiently to stimuli such as nutrient availability or the presence of toxins. However, the search process is hindered by slow diffusive movement and the presence of 'false' targets - DNA segments that are similar to the true target. In eukaryotic cells, most TFs contain an intrinsically disordered region (IDR), which is commonly assumed to behave as a long, flexible polymeric tail composed of hundreds of amino acids. Recent experimental findings indicate that the IDR of certain TFs plays a pivotal role in the search process. However, the principles underlying the IDR's role remain unclear. Here, we reveal key design principles of the IDR related to TF binding affinity and search time. Our results demonstrate that the IDR significantly enhances both of these aspects. Furthermore, our model shows good agreement with experimental results, and we propose further experiments to validate the model's predictions.
    Keywords:  S. cerevisiae; intrinsically disordered regions; physics of living systems; polymer physics; statistical physics; transcription factors
    DOI:  https://doi.org/10.7554/eLife.104956
  9. Nat Genet. 2025 Oct 03.
    Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq.
    Wangjie Liu, Wouter Saelens, Pernille Rainer, Marjan Biočanin, Vincent Gardeux, Antoni Jakub Gralak, Guido van Mierlo, Angelika Gebhart, Julie Russeil, Tingdang Liu, Wanze Chen, Bart Deplancke.
      Reprogramming often yields heterogeneous cell fates, yet the underlying mechanisms remain poorly understood. To address this, we developed single-cell transcription factor sequencing (scTF-seq), a single-cell technique that induces barcoded, doxycycline-inducible TF overexpression and quantifies TF dose-dependent transcriptomic changes. Applied to mouse embryonic multipotent stromal cells, scTF-seq generated a gain-of-function atlas for 384 mouse TFs, identifying key regulators of lineage specification, cell cycle control and their interplay. Leveraging single-cell resolution, we uncovered how TF dose shapes reprogramming heterogeneity, revealing both dose-dependent and stochastic cell state transitions. We classified TFs into low-capacity and high-capacity groups, with the latter further subdivided by dose sensitivity. Combinatorial scTF-seq demonstrated that TF interactions can shift from synergistic to antagonistic depending on the relative dose. Altogether, scTF-seq enables the dissection of TF function, dose and cell fate control, providing a high-resolution framework to understand and predict reprogramming outcomes, advancing gene regulation research and the design of cell engineering strategies.
    DOI:  https://doi.org/10.1038/s41588-025-02343-7
  10. Mol Cell. 2025 Oct 02. pii: S1097-2765(25)00714-2. [Epub ahead of print]85(19): 3554-3561
    A needed nomenclature for nucleosomes.
    Michael-Christopher Keogh, Genevieve Almouzni, Andrew J Andrews, Karim-Jean Armache, Cheryl H Arrowsmith, Sung Hee Baek, Mark T Bedford, Emily Bernstein, Jacques Côté, Yael David, John M Denu, Beat Fierz, Benjamin A Garcia, Karen C Glass, Or Gozani, Kristian Helin, Steven Henikoff, Ole N Jensen, Steven Z Josefowicz, Neil L Kelleher, Tatiana G Kutateladze, Herbert H Lindner, Chao Lu, Karolin Luger, Parag Mallick, Catherine A Musselman, Tom W Muir, Ljiljana Paša-Tolić, Robert Schneider, Xiaobing Shi, Yang Shi, Simone Sidoli, Lloyd M Smith, Jessica K Tyler, Cynthia Wolberger, Jerry L Workman, Brian D Strahl, Nicolas L Young.
      Histone post-translational modifications (PTMs) are crucial to eukaryotic genome regulation, with a range of reported functions and mechanisms of action. Though often studied individually, it has long been recognized that the modifications function by combinatorial synergy or antagonism. Interplay may involve PTMs on the same histone, within the same nucleosome (containing a histone octamer), or between nucleosomes in higher-order chromatin. Given this, the field must distinguish ever greater complexity, and the context in which it is studied, with brevity and precision. The proteoform was introduced to define individual forms of a protein by sequence and PTMs, followed by the nucleoform to describe the particular gathering of histones within an individual nucleosome. There is now a need to define specific forms of these entities in prose while providing space for experimental nuance. To this end, we introduce a nomenclature that can express discrete PTMs, proteoforms, nucleoforms, or situations where defined PTMs exist in an uncertain context. Though specifically designed for the chromatin field, adaptions of the framework could be used to describe-and thus dissect-how proteoforms are configured in functionally distinct complexes across biology.
    DOI:  https://doi.org/10.1016/j.molcel.2025.08.029
  11. Cell. 2025 Sep 26. pii: S0092-8674(25)01034-7. [Epub ahead of print]
    Single-cell nascent transcription reveals sparse genome usage and plasticity.
    Shaoqian Ma, Yantao Hong, Junhan Chen, Jingzhao Xu, Xiaohua Shen.
      Understanding cell diversification from a common genome in metazoans requires single-cell transcriptional analysis. We introduce single-cell full-length EU-labeled nascent RNA sequencing (scFLUENT-seq), a single-cell nascent RNA sequencing method using brief 10-min metabolic labeling to capture genome-wide transcription. Surprisingly, individual cells-from splenic lymphocytes to pluripotent stem cells-transcribe only ∼0.02%-3.1% of the genome, versus >80% in bulk, revealing limited genome engagement and profound cell-type and cell-to-cell heterogeneity. Intergenic transcription, especially from heterochromatin, is pervasive and stochastic. Promoter-associated antisense and genic transcription rarely co-occur in the same cell. Proximal intergenic transcription involves both gene readthrough and independent initiation, while distal intergenic transcription is largely independent of neighboring genes and correlates with increased transcriptional diversity, a hallmark of cellular plasticity. Although global RNA synthesis and turnover are coupled in bulk, individual mRNA transcription and decay are poorly coordinated in single cells, suggesting noise-buffering mechanisms. Overall, scFLUENT-seq uncovers complex coding and noncoding transcriptional dynamics that underlie single-cell heterogeneity and state transitions.
    Keywords:  cell state and plasticity; chromatin; heterogeneity; noncoding genome; single-cell nascent RNA-seq; transcription dynamics
    DOI:  https://doi.org/10.1016/j.cell.2025.09.003
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