bims-crepig 2025-09-21 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2025–09–21
eleven papers selected by
Connor Rogerson, University of Cambridge

Requirements for establishment and epigenetic stability of mammalian heterochromatin.
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene.
The histone chaperone Spt6 controls chromatin structure through its conserved N-terminal domain.
FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data.
INO80/SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape.
Reorganization of H3K9me2-modified chromatin regions during mouse embryonic development.
SMRT anchors the HDAC3 corepressor complex to chromatin to regulate inflammatory and metabolic pathways in macrophages.
A hierarchical, count-based model highlights challenges in scATAC-seq data analysis and points to opportunities to extract finer-resolution information.
3D chromatin structures precede genome activation in Drosophila embryogenesis.
Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation.
Phosphorylation of H3.3 at Serine 31 acts as a switch of nucleosome dynamics for transcription.

Mol Cell. 2025 Sep 18. pii: S1097-2765(25)00710-5. [Epub ahead of print]85(18): 3388-3406.e12

Requirements for establishment and epigenetic stability of mammalian heterochromatin.

Antonis Tatarakis, Harleen Saini, Juntao Yu, Wenzhi Feng, Carlos A Pinzon-Arteaga, Danesh Moazed.

  Heterochromatic domains of DNA account for a large fraction of mammalian genomes and play critical roles in silencing transposons and genes, but the mechanisms that establish and maintain these domains are not fully understood. Here, we use a CRISPR-based genetic screen to investigate the requirements for establishment and maintenance of histone H3 lysine 9 trimethylation (H3K9me3) heterochromatin. In mouse embryonic stem cells (mESCs), we show that transiently induced H3K9me3 heterochromatin is inherited for a limited number of cell divisions, independently of sequence-dependent recruitment, but becomes stable upon differentiation, concomitant with downregulation of enzymes erasing H3K9me and DNA methylation. In addition, ordered and non-redundant activities of multiple H3K9 and DNA methyltransferases, together with histone deacetylases, chromatin remodeling complexes, and RNA processing factors, are required for heterochromatin maintenance. Our findings suggest that a newly acquired H3K9me3 domain can be maintained like an imprint but requires reinforcement by DNA methylation and other pathways.

Keywords:  CRISPR screen; DNA methylation; H3K9me3; Polycomb; epigenetic inheritance; heterochromatin; imprinting; mESCs

DOI:  https://doi.org/10.1016/j.molcel.2025.08.025
Science. 2025 Sep 18. 389(6766): eads6552

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene.

Mathias Eder, Christina J I Moene, Lise Dauban, Mikhail Magnitov, Jamie Drayton, Marcel de Haas, Christ Leemans, Martijn Verkuilen, Elzo de Wit, Anders S Hansen, Bas van Steensel.

Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alternative positions within a single locus, we dissected the positional relationship between the mouse Sox2 gene and its distal enhancer. This revealed an intricate, sharply confined activation landscape in which the native Sox2 gene occupies an optimal position for its activation. Deletion of the gene relaxes this confinement and broadly increases reporter activity. The confining effect of the Sox2 gene is partially conferred by its ~1-kilobase coding region. Our local relocation approach provides high-resolution functional maps of a genomic locus and reveals that a gene can strongly constrain the realm of influence of its enhancer.

DOI: https://doi.org/10.1126/science.ads6552
Mol Cell. 2025 Sep 18. pii: S1097-2765(25)00705-1. [Epub ahead of print]85(18): 3407-3424.e8

The histone chaperone Spt6 controls chromatin structure through its conserved N-terminal domain.

James L Warner, Vanda Lux, Václav Veverka, Fred Winston.

  The disassembly and reassembly of nucleosomes by histone chaperones is an essential activity during eukaryotic transcription elongation. This highly conserved process maintains chromatin integrity by transiently removing nucleosomes as barriers and then restoring them in the wake of transcription. While transcription elongation requires multiple histone chaperones, there is little understanding of how most of them function and why so many are required. Here, we show that the histone chaperone Spt6 acts through its acidic, intrinsically disordered N-terminal domain (NTD) to bind histones and control chromatin structure. The Spt6 NTD is essential for viability, and its histone-binding activity is conserved between yeast and humans. The essential nature of the Spt6 NTD can be bypassed by changes in another histone chaperone, FACT, revealing a close functional connection between the two. Our results have led to a mechanistic model for dynamic cooperation between multiple histone chaperones during transcription elongation.

Keywords:  Elf1; FACT; IDR; RNA polymerase II; Spn1; Spt6; histone chaperones; histones; nucleosomes; transcription elongation

DOI:  https://doi.org/10.1016/j.molcel.2025.08.020
Bioinformatics. 2025 Sep 17. pii: btaf502. [Epub ahead of print]

FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data.

Guido Barzaghi, Arnaud R Krebs, Judith B Zaugg.

SUMMARY: Single molecule footprinting profiles the heterogeneity of TF occupancy at cis-regulatory elements across cell populations at unprecedented resolution. The single molecule nature of the data in principle allows for observing the footprint of individual transcription factors and nucleosomes. However, we currently lack algorithms to quantify these occupancy patterns of chromatin binding factors in an automated way and without prior assumptions on their genomic location. Here we present FootprintCharter, an unsupervised tool to detect and quantify footprints for transcription factors (TFs) and nucleosomes from single molecule footprinting data. After detection, TF footprints can be labelled with orthogonal motif annotations provided by the user. FootprintCharter allows for the quantification of complex molecular states such as positioning of unphased nucleosomes and combinatorial co-binding of multiple TFs.
AVAILABILITY AND IMPLEMENTATION: FootprintCharter is freely available on Bioconductor with version 2.2.0 of https://bioconductor.org/packages/SingleMoleculeFootprinting through the functions FootprintCharter, PlotFootprints and Plot_FootprintCharter_SM.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btaf502
Nucleic Acids Res. 2025 Sep 05. pii: gkaf892. [Epub ahead of print]53(17):

INO80/SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape.

Meitong Liu, Qiqin Xu, Hui Wang, Xiong Ji.

INO80/SWR remodelers, including INO80, P400/TIP60, and SRCAP, have been viewed to regulate H2A.Z dynamics, but how they control specific gene expression remains unclear. Here, we reveal distinct phenotypes arising from short- and long-term perturbations following the depletion of INO80/SWR remodelers. We identified the direct target genes of INO80, P400, and SRCAP remodelers. Mechanistically, we found that INO80/SWR remodelers interact and facilitate the chromatin occupancy of the H2A.Zac reader protein BRD2, thereby elucidating the regulation of Pol II transcription by INO80/SWR remodelers. Additionally, while the degradation of P400 or SRCAP led to a reduction in H2A.Zac, INO80 depletion did not affect H2A.Zac occupancy but decreased the occupancy of P400 and SRCAP. Collectively, our findings suggest that INO80/SWR remodelers primarily regulate the chromatin landscape and influences BRD2 chromatin binding, thereby shedding light on their mechanisms in Pol II transcription regulation during development and disease.

DOI: https://doi.org/10.1093/nar/gkaf892
Dev Biol. 2025 Sep 17. pii: S0012-1606(25)00260-X. [Epub ahead of print]

Reorganization of H3K9me2-modified chromatin regions during mouse embryonic development.

Diana Fulmer, Emily J Shields, Andrey Poleshko, Jonathan A Epstein, Cheryl L Smith.

  The three-dimensional organization of chromatin in the nucleus is critical in regulating gene expression. There are two classes of large genomic regions demarcated by the repressive chromatin modification histone H3 lysine 9 dimethyl (H3K9me2) and enriched at the nuclear periphery: lamina-associated domains (LADs); and H3K9me2-only domains (KODs) which have minimal lamina contact and are highly enriched for transcriptional enhancers. LADs have been studied in multiple cell types. In contrast, KODs have been characterized only in pluripotent cells and it remains to be determined whether they are fixed or rearrange according to cell type. Analysis of KODs from various embryonic mouse tissues revealed that KODs adopt cell type-specific configurations that correlate with changes in lineage-specific enhancer activity. Within KODs, local cell type-specific depletion of H3K9me2 was enriched for H3K27ac peaks at active lineage-specific enhancers. KODs were also enriched across ultra-long regulatory regions suggesting a role for KODs in long-range gene regulation. These results suggest that KODs are cell-type specific and maintain cell type-specific enhancers in a repressed state to allow for tissue- and stage-specific gene activation.

Keywords:  Enhancer; H3K9me2; gene regulation; lamina; nuclear architecture

DOI:  https://doi.org/10.1016/j.ydbio.2025.09.005
Nucleic Acids Res. 2025 Sep 05. pii: gkaf880. [Epub ahead of print]53(17):

SMRT anchors the HDAC3 corepressor complex to chromatin to regulate inflammatory and metabolic pathways in macrophages.

Astradeni Efthymiadou, Chaode Gu, Cheng Wang, Hongwei Wang, Ziyi Li, Oihane Garcia-Irigoyen, Rongrong Fan, Eckardt Treuter, Zhiqiang Huang.

Transcription factors and coregulators coordinate inflammatory and metabolic pathways in macrophages through epigenetic and transcriptional mechanisms. The histone deacetylase 3 (HDAC3) corepressor complex plays fundamental roles in these mechanisms, with the homologous subunits SMRT (silencing mediator of retinoic acid and thyroid hormone receptors) and NCOR (nuclear receptor corepressor) being critical for complex assembly and interactions with transcription factors and chromatin. However, the relative contribution of SMRT and NCOR in controlling complex-dependent macrophage pathways remains poorly understood. Here, we assessed their genome-wide roles in mouse macrophage RAW264.7 cells and in bone marrow-derived macrophages. Transcriptome analysis upon corepressor depletion identified six differentially expressed gene clusters. SMRT depletion primarily upregulated inflammation-related pathways, whereas NCOR depletion primarily upregulated metabolism-related pathways. Epigenome analysis revealed that corepressor depletion differentially altered chromatin accessibility and H3K27 acetylation, consistent with transcriptome changes. Cistrome analysis revealed that both corepressors differentially influence each other at chromatin. SMRT uniquely controls the chromatin binding and nuclear localization of NCOR, GPS2 (G protein pathway suppressor 2), and HDAC3, thus acting as the chromatin anchor for the corepressor complex. Finally, corepressor depletion differentially modulated macrophage reprogramming in response to TLR4, IL4, and LXR signaling. Overall, our study reveals a hitherto underappreciated non-redundant role of SMRT and NCOR in coordinating chromatin accessibility, H3K27 acetylation, enhancer activity, and transcription to differentially regulate inflammatory and metabolic macrophage pathways.

DOI: https://doi.org/10.1093/nar/gkaf880
Genome Biol. 2025 Sep 17. 26(1): 282

A hierarchical, count-based model highlights challenges in scATAC-seq data analysis and points to opportunities to extract finer-resolution information.

Aaron Wing Cheung Kwok, Heejung Shim, Davis J McCarthy.

BACKGROUND: Data from Single-cell Assay for Transposase Accessible Chromatin with Sequencing (scATAC-seq) is highly sparse. While current computational methods feature a range of transformation procedures to extract meaningful information, major challenges remain.
RESULTS: Here, we discuss the major scATAC-seq data analysis challenges such as sequencing depth normalization and region-specific biases. We present a hierarchical count model that is motivated by the data generating process of scATAC-seq data. Our simulations show that current scATAC-seq data, while clearly containing physical single-cell resolution, are too sparse to infer true informational-level single-cell, single-region of chromatin accessibility states.
CONCLUSIONS: While the broad utility of scATAC-seq at a cell type level is undeniable, describing it as fully resolving chromatin accessibility at single-cell resolution, particularly at individual locus level, may overstate the level of detail currently achievable. We conclude that chromatin accessibility profiling at true single-cell, single-region resolution is challenging with current data sensitivity, but that it may be achieved with promising developments in optimizing the efficiency of scATAC-seq assays.

DOI: https://doi.org/10.1186/s13059-025-03735-y
Cell Genom. 2025 Sep 15. pii: S2666-979X(25)00258-7. [Epub ahead of print] 101002

3D chromatin structures precede genome activation in Drosophila embryogenesis.

Gabriel A Dolsten, Evan M Cofer, Xin Yang Bing, Benjamin Brack, Marcus Curlin, Chandra L Theesfeld, Olga G Troyanskaya, Michael S Levine, Yuri Pritykin.

  3D chromatin structure is critical for the regulation of gene expression during development. Here we used Micro-C assays at 100-bp resolution to map genome organization in Drosophila melanogaster throughout the first half of embryogenesis. These high-resolution contact maps reveal fine-scale features such as loops and boundaries delineating topologically associating domains. Notably, we observe that 3D chromatin structures form prior to zygotic genome activation and persist during successive mitotic cycles. Integrative analysis with 149 public chromatin immunoprecipitation sequencing (ChIP-seq) datasets identifies four classes of chromatin structuring elements, including a distinct group enriched for GAGA-associated factor (GAF) and Zelda binding, associated with developmental-gene regulation. These elements are mitotically retained and exhibit sequence and structure similarity between D. melanogaster and D. virilis. We propose that 3D chromatin organization in the pre-cellular embryo facilitates deployment of developmentally regulated genes during Drosophila embryogenesis.

Keywords:  ChIP-seq; Drosophila; Micro-C; TAD; chromatin boundaries; chromatin loops; clustering; computation; development; embryo; insulators; nucleosome

DOI:  https://doi.org/10.1016/j.xgen.2025.101002
Nucleic Acids Res. 2025 Sep 05. pii: gkaf918. [Epub ahead of print]53(17):

Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation.

Ahmad Alshehri, India-May Baker, David M English, Louise Fairall, Mark O Collins, John W R Schwabe, Shaun M Cowley.

Histone deacetylase 1 and 2 (HDAC1/2) regulate histone acetylation as catalytic and structural components of six unique multiprotein complex families: SIN3, NuRD, CoREST, MIDAC, MIER, and RERE. Co-immunoprecipitation of HDAC1-Flag followed by mass spectrometry revealed that 92% of HDAC1 in mouse embryonic stem cells resides in three complexes, NuRD (49%), CoREST (28%), and SIN3 (15%). We compared the structures of MTA1:HDAC1 and MIDEAS:HDAC1 to identify critical binding residues on the surface of HDAC1. Surprisingly, a single mutation, Y48E, disrupts binding to all complexes except SIN3. Rescue experiments performed with HDAC1-Y48E in HDAC1/2 double-knockout cells showed that retention of SIN3 binding alone is sufficient for cell viability. Gene expression and histone acetylation patterns were perturbed in both Y48E and a second mutant cell line, HDAC1-E63R, indicating that cells require a full repertoire of the HDAC1/2 complexes to regulate their transcriptome appropriately. Comparative analysis of MTA1/HDAC1 and SIN3B/HDAC2 structures confirmed the differential modes of HDAC1 recruitment, with Y48 interacting with ELM2/SANT domain-containing proteins, but not SIN3. The E63R mutation shows markedly reduced binding to NuRD and MiDAC complexes but retains some CoREST binding. We provide novel molecular insights into the abundance, co-factors and assemblies of this crucial family of chromatin modifying machines.

DOI: https://doi.org/10.1093/nar/gkaf918
Nucleic Acids Res. 2025 Sep 05. pii: gkaf891. [Epub ahead of print]53(17):

Phosphorylation of H3.3 at Serine 31 acts as a switch of nucleosome dynamics for transcription.

Jingzhe Ma, Junran Zhang, Xue Xiao, Li Gao, Hang Zhou, Dengyu Ji, Ying Zhang, Guohong Li, Juan Yu, Ping Chen, Wei Li.

The incorporation of histone variant H3.3 into the genome plays a critical role in regulating gene transcription, genomic stability, and mitosis progression. However, the precise mechanisms underlying the influence of H3.3 on nucleosome stability and dynamics remain poorly understood. In this study, we demonstrate that while the incorporation of H3.3 into nucleosomes does not significantly alter their stability, it enhances the maintenance of nucleosome integrity. Notably, H3.3 recruits the FACT complexes more efficiently than the canonical H3, counteracting FACT's destabilizing effect on nucleosomes. The binding of FACT to H3.3-nucleosome further stabilizes the nucleosome structure, which can be reversed by phosphorylation at Serine 31 (H3.3S31ph). Through genome-wide analyses, we show that the deposition of H3.3 and its phosphorylation at Ser31 dynamically modulate the nucleosome states, influencing FACT binding and regulating the transcriptional responses in macrophages upon stimulation. The selective phosphorylation at H3.3S31 functions as a pivotal switch, transforming the H3.3-nucleosome from a stable, maintenance-oriented state to a more dynamic, active configuration. This molecular switch enables a rapid response to environmental stimuli, thereby facilitating transcriptional activation. Our findings provide new mechanistic insights into how H3.3 and its Ser31 phosphorylation modulate nucleosome dynamics and transcriptional response, with significant implications for immune response pathways in macrophages.

DOI: https://doi.org/10.1093/nar/gkaf891