bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2025–08–10
27 papers selected by
Connor Rogerson, University of Cambridge



  1. Sci Adv. 2025 Aug 08. 11(32): eadt2002
      The histone variant H2A.Z marking permissive chromatin is deposited by the multicomponent SWR1 chromatin remodeler, which is targeted to nucleosome-free promoters by a DNA length-sensing module. How SWR1 is directed to the flanking acetylated +1 nucleosome, its physiological substrate, has been enigmatic. We show by live-cell, single-molecule tracking that SWR1 subunits Bdf1 and Yaf9 harboring histone acetylation reader domains differentially regulate chromatin binding: Bdf1 promotes SWR1 association, while Yaf9-YEATS slows its dissociation. Notably, single-molecule tracking and genome-wide chromatin immunoprecipitation combined with exonuclease treatment reveal Bdf1 and Yaf9 contributions to global SWR1 targeting and histone exchange at +1 nucleosomes. Our findings highlight the in-cell biochemistry of histone readers and suggest a generalizable, two-stage mechanism wherein acetylated nucleosome interactions initially constrain the three-dimensional diffusion of SWR1 to increase local concentration, followed by stochastic one-dimensional diffusion at nucleosome-depleted regions with directional capture by acetylated +1 nucleosomes.
    DOI:  https://doi.org/10.1126/sciadv.adt2002
  2. Mol Cell. 2025 Aug 07. pii: S1097-2765(25)00606-9. [Epub ahead of print]85(15): 2900-2918.e16
      Transcription factors (TFs) recognizing DNA motifs within regulatory regions drive cell identity. Despite recent advances, their specificity remains incompletely understood. Here, we address this by contrasting two TFs, Neurogenin-2 (NGN2) and MyoD1, which recognize ubiquitous E-box motifs yet drive distinct cell fates toward neurons and muscles, respectively. Upon induction in mouse embryonic stem cells, we monitor binding across differentiation, employing an interpretable machine learning approach that integrates preexisting DNA accessibility. This reveals a chromatin-dependent motif syntax, delineating both common and factor-specific binding, validated by cellular and in vitro assays. Shared binding sites reside in open chromatin, locally influenced by nucleosomes. In contrast, factor-specific binding in closed chromatin involves NGN2 and MyoD1 acting as pioneer factors, influenced by motif variant frequencies, motif spacing, and interaction partners, which together account for subsequent lineage divergence. Transferring our methodology to other models demonstrates how a combination of opportunistic binding and context-specific chromatin-opening underpin TF specificity, driving differentiation trajectories.
    Keywords:  E-box; cell differentiation; chromatin accessibility; gene regulation; machine learning; motif syntax; motif variants; pioneer factors; predictive models; transcription factor specificity
    DOI:  https://doi.org/10.1016/j.molcel.2025.07.005
  3. Cell Rep. 2025 Aug 06. pii: S2211-1247(25)00892-7. [Epub ahead of print]44(8): 116121
      Transcription factors (TFs) regulate gene expression despite constraints from chromatin structure and the cell cycle. Here, we examine the concentration-dependent regulation of hunchback by the Bicoid morphogen through a combination of quantitative imaging, mathematical modeling, and epigenomics in Drosophila embryos. By live imaging of MS2 reporters, we find that, following mitosis, the timing of transcriptional activation driven by the hunchback P2 (hbP2) enhancer directly reflects Bicoid concentration. We build a stochastic model that can explain in vivo onset time distributions by accounting for both the competition between Bicoid and nucleosomes at hbP2 and a negative influence of DNA replication on transcriptional elongation. Experimental modulation of nucleosome stability alters onset time distributions and the posterior boundary of hunchback expression. We conclude that TF-nucleosome competition is the molecular mechanism whereby the Bicoid morphogen gradient specifies the posterior boundary of hunchback expression.
    Keywords:  CP: Developmental biology; CP: Molecular biology; DNA replication; Drosophila; Embryonic patterning; MS2 reporter; chromatin; computational modeling; morphogen; nucleosome; transcription factor
    DOI:  https://doi.org/10.1016/j.celrep.2025.116121
  4. Nat Commun. 2025 Aug 08. 16(1): 7313
      Chromatin signatures are widely used to identify tissue-specific in vivo enhancers, but their sensitivity and specificity remains unclear. Here we show that many developmental enhancers remain undetectable using currently available chromatin data. In an initial comparison of over 1200 developmental enhancers with tissue-matched chromatin data, 14% (n = 285) lacked canonical enhancer-associated chromatin signatures. To further assess the prevalence of enhancers missed by chromatin profiling approaches, we used a high-throughput transgenic enhancer assay to screen the regulatory landscapes of two key developmental genes at 5 kb resolution, spanning 1.3 Mb of mouse sequence in total. We observed that 23 of 88 (26%) in vivo enhancers discovered by this approach lacked enhancer-associated chromatin signatures in the respective tissue. Our findings suggest the existence of tens of thousands of enhancers that remain undiscovered by currently available chromatin data, underscoring the continued need for expanding resources for enhancer discovery.
    DOI:  https://doi.org/10.1038/s41467-025-62497-0
  5. Sci Adv. 2025 Aug 08. 11(32): eadu3308
      Profiling combinations of histone modifications identifies gene regulatory elements in different states and discovers features controlling transcriptional and epigenetic programs. However, efforts to map chromatin states in complex, heterogeneous samples are hindered by the lack of methods that can profile multiple histone modifications together with transcriptomes in individual cells. Here, we describe single-cell multitargets and mRNA sequencing (scMTR-seq), a high-throughput method that enables simultaneous profiling of six histone modifications and transcriptome in single cells. We apply scMTR-seq to uncover dynamic and coordinated changes in chromatin states and transcriptomes during human endoderm differentiation. We also use scMTR-seq to produce lineage-resolved chromatin maps and gene regulatory networks in mouse blastocysts, revealing epigenetic asymmetries at gene regulatory regions between the three embryo lineages and identifying Trps1 as a potential repressor in epiblast cells of trophectoderm-associated enhancer networks and their target genes. Together, scMTR-seq enables investigation of combinatorial chromatin landscapes in a broad range of heterogeneous samples, providing insights into epigenetic regulatory systems.
    DOI:  https://doi.org/10.1126/sciadv.adu3308
  6. Nat Commun. 2025 Aug 02. 16(1): 7118
      Transcription factors (TFs) and transcriptional coregulators are emerging therapeutic targets. Gene regulatory networks (GRNs) can evaluate pharmacological agents and identify drivers of disease, but methods that rely solely on gene expression often neglect post-transcriptional modulation of TFs. We present Epiregulon, a method that constructs GRNs from single-cell ATAC-seq and RNA-seq data for accurate prediction of TF activity. This is achieved by considering the co-occurrence of TF expression and chromatin accessibility at TF binding sites in each cell. ChIP-seq data allows motif-agonistic activity inference of transcriptional coregulators or TF harboring neomorphic mutations. Epiregulon accurately predicted the effects of AR inhibition across different drug modalities including an AR antagonist and an AR degrader, delineated the mechanisms of a SMARCA4 degrader by identifying context-dependent interaction partners, and prioritized drivers of lineage reprogramming and tumorigenesis. By mapping gene regulation across various cellular contexts, Epiregulon can accelerate the discovery of therapeutics targeting transcriptional regulators.
    DOI:  https://doi.org/10.1038/s41467-025-62252-5
  7. Genome Res. 2025 Aug 05. pii: gr.280732.125. [Epub ahead of print]
      The three-dimensional (3D) genome structure is essential for gene regulation and various genomic functions. CTCF plays a key role in organizing Topologically Associated Domains (TADs) and promoter-enhancer loops, contributing to proper cell differentiation and development. Although CTCF binds the genome with high sequence specificity, its binding sites are dynamically regulated during development, and aberrant CTCF binding is linked to diseases such as cancer and neurological disorders, and aging. However, the mechanisms controlling CTCF binding remain unclear. Here, we investigate the role of repressive chromatin modifications in CTCF binding using H3K9 methyltransferase-deficient immortalized mouse embryonic fibroblasts (iMEFs) and H3K27 methyltransferase EZH1/2 inhibitor. We find that H3K9 and H3K27 methylation regulate CTCF binding at distinct genomic regions, and their simultaneous loss induces drastic changes in CTCF binding. These changes are associated with alterations in 3D genome architecture and gene expression, suggesting that repressive chromatin modifications preserve proper chromatin organization by preventing aberrant CTCF binding. Additionally, while CTCF binding sites repressed by H3K9 methylation are bound by CTCF in early mouse embryos, those repressed by both H3K9 and H3K27 methylation remain inaccessible, with early embryonic-specific H3K27 methylation forming at these sites. These findings implicate that H3K27 methylation plays a role for restricting CTCF binding in early embryos, ensuring proper genome organization during development.
    DOI:  https://doi.org/10.1101/gr.280732.125
  8. Mol Cell. 2025 Aug 07. pii: S1097-2765(25)00607-0. [Epub ahead of print]85(15): 2937-2955.e10
      The mechanisms by which the expression of pluripotency and Polycomb networks are harmonized to allow the transition from pluripotency to a differentiated state have not been fully elucidated. Integrator complex regulates transcription pause release and RNA processing in metazoans. We show that Integrator is required for stemness and plays a critical role as early as day 2 in embryonic development. While the catalytic endonuclease activity enhances cellular reprogramming, Integrator recruits RNA polymerase II (RNAPII) to promoters and super enhancers of pluripotency and Polycomb genes. Integrator coordinates expression of pluripotency and Polycomb networks by fostering the association of RNAPII and basal transcription factors. We pinpoint a critical role for TATA-binding protein-associated factors (TAFs) in Integrator entry into the preinitiation complex. Taken together, beyond its role in RNAPII pause release, Integrator recruitment of RNAPII ensures an orderly cellular differentiation during development.
    Keywords:  Integrator; RNA polymerase II recruitment; basal transcription factors; cellular differentiation; development; embryonic stem cells; enhancer; pluripotency; promoter; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2025.07.006
  9. Sci Adv. 2025 Aug 08. 11(32): eadw0126
      Bone fracture repair initiates by periosteal expansion. The periosteum is a bilayered tissue composed of inner cambium and outer fibrous layers. Typically quiescent, periosteal progenitor cells proliferate upon fracture; however, the underlying transcriptional mechanisms remain unclear. Here, we show that deletion of the transcriptional regulators, yes-associated protein (YAP) and transcriptional coactivator with PDZ binding motif (TAZ), from Osterix-expressing cells, which reside in the cambium, impairs periosteal expansion. YAP activation increases chromatin accessibility, preferentially at TEA domain transcription factor (TEAD) binding sites, and regulates both cell-intrinsic and cell-extrinsic cellular functions. We identify bone morphogenetic protein 4 (Bmp4) as a YAP-TEAD target gene expressed in the cambium. In YAP/TAZ knockout mice, BMP4 delivery increased periosteal expansion through matrix accumulation and fibrous layer cell proliferation. Conversely, in wild-type mice, BMP4 delivery increased osteogenic activity and angiogenesis. Together, these data identify YAP-mediated transcriptional programs that promote layer-specific periosteal expansion.
    DOI:  https://doi.org/10.1126/sciadv.adw0126
  10. Nat Struct Mol Biol. 2025 Aug 05.
      The search for target sites on chromatin by eukaryotic sequence-specific transcription factors (TFs) is integral to the regulation of gene expression but the mechanism of nuclear exploration has remained obscure. Here we use multicolor single-molecule fluorescence resonance energy transfer and single-particle imaging to track the diffusion of purified Drosophila GAGA factor (GAF) on DNA and nucleosomes. Monomeric GAF DNA-binding domain (DBD) bearing one zinc finger finds its cognate site through one-dimensional (1D) or three-dimensional (3D) diffusion on bare DNA and rapidly slides back and forth between naturally clustered motifs for seconds before dissociation. Multimeric, full-length GAF also finds clustered motifs on DNA through 1D-3D diffusion but remains locked on target for longer periods. Nucleosome architecture effectively blocks GAF-DBD 1D sliding into the histone core but favors retention of GAF-DBD once it has bound to a solvent-exposed motif through 3D diffusion. Despite the occlusive nature of nucleosomes, 1D-3D facilitated diffusion enables GAF to effectively search for clustered cognate motifs in chromatin, providing a mechanism for navigation to nucleosomal and nucleosome-free sites by a member of the zinc finger TF family.
    DOI:  https://doi.org/10.1038/s41594-025-01643-0
  11. Nat Genet. 2025 Aug 06.
      Cell atlas projects have revealed that common cell types often comprise distinct, recurrent transcriptional states, but the function and regulation of these states remain poorly understood. Here, we show that systematic activation of transcription factors can recreate such states in vitro, providing tractable models for mechanistic and functional studies. Using a scalable CRISPR activation (CRISPRa) Perturb-seq platform, we activated 1,836 transcription factors in two cell types. CRISPRa induced gene expression within physiological ranges, with chromatin features predicting responsiveness. Comparisons with atlas datasets showed that transcription factor perturbations recapitulated key fibroblast states and identified their regulators, including KLF2 and KLF4 for a universal state present in many tissues, and PLAGL1 for a disease-associated inflammatory state. Inducing the universal state suppressed the inflammatory state, suggesting therapeutic potential. These findings position CRISPRa as a nuanced tool for perturbing differentiated cells and establish a general strategy for studying clinically relevant transcriptional states ex vivo.
    DOI:  https://doi.org/10.1038/s41588-025-02284-1
  12. Sci Rep. 2025 Aug 06. 15(1): 28672
      Genome-wide profiling of DNA-protein interactions in cells can provide important information about mechanisms of gene regulation. Most current methods for genome-wide profiling of DNA-bound proteins such as ChIP-seq and CUT&Tag use conventional IgG antibodies to bind the target protein(s). This limits their applicability to targets with available high affinity and specificity antibodies and prevents their use for other targets. Here we describe NanoTag, an IgG-free method derived from CUT&Tag to profile DNA-protein interactions. NanoTag is based on a fusion between an anti-GFP nanobody and Tn5 transposase that can map GFP-tagged proteins associated with chromatin in a fast, cost-effective and animal-free manner. We used NanoTag to indirectly profile the histone mark H3K4me3 genome-wide via its binding partner TATA box-binding protein-associated factor 3 (TAF3) and the transcription factors Nanog and CTCF in mouse embryonic stem cells (mESCs). NanoTag results show high inter-replicate reproducibility, high signal-to-noise ratio and strong correlation with CUT&Tag datasets, validating its accuracy and reliability. NanoTag provides a novel, flexible and cost-effective IgG-free method to generate high resolution DNA-binding profiles in cells and tissues.
    Keywords:  CUT&Tag; Chromatin; Chromatin profiling; DNA–protein interactions; Epigenomics; Nanobody; Tn5 tagmentation
    DOI:  https://doi.org/10.1038/s41598-025-13316-5
  13. Genes Dev. 2025 Aug 06.
      Regulators of chromatin accessibility play key roles in cell fate transitions, triggering the onset of novel transcription programs as cells differentiate. In the Drosophila male germline stem cell lineage, tMAC, a master regulator of spermatocyte differentiation that binds thousands of loci, is required for local opening of chromatin, allowing activation of spermatocyte-specific promoters. Here we show that a cell type-specific surveillance system involving the multiple zinc finger protein Kmg and the pipsqueak domain protein Dany dampens transcriptional output from weak tMAC-dependent promoters and counteracts tMAC binding at thousands of additional cryptic promoters, thus preventing massive expression of aberrant protein-coding transcripts. ChIP-seq showed Kmg enriched at the tMAC-bound promoters that it repressed, consistent with direct action. In contrast, Kmg and Dany did not repress highly expressed tMAC-dependent genes, where they colocalized with their binding partner, the chromatin remodeler Mi-2 (NuRD), along the transcribed regions rather than at the promoter. We discuss a model where Kmg, together with Dany and Mi-2, dampens expression from weak or ectopic promoters while allowing robust transcription from highly expressed Aly-dependent genes.
    Keywords:  Drosophila; NuRD complex; chromatin regulation; cryptic promoters; spermatogenesis; transcriptional repression
    DOI:  https://doi.org/10.1101/gad.352747.125
  14. Cell Rep. 2025 Jul 31. pii: S2211-1247(25)00860-5. [Epub ahead of print]44(8): 116089
      The cell cycle is a tightly regulated process that requires precise temporal expression of thousands of cell-cycle-dependent genes. However, the genome-wide dynamics of mRNA metabolism throughout the cell cycle remain uncharacterized. Here, we combined single-cell multiome sequencing, biophysical modeling, and deep learning to quantify rates of mRNA transcription, splicing, nuclear export, and degradation. Our approach revealed that both transcriptional and post-transcriptional processes exhibit distinct oscillatory waves at specific cell cycle phases, with post-transcriptional regulation playing a prominent role in shaping mRNA accumulation. We also observed dynamic changes in chromatin accessibility and transcription factor binding footprints, identifying key regulators underlying the oscillatory dynamics of mRNA. Taken together, the results of our approach uncovered a high-resolution map of RNA metabolism dynamics and chromatin accessibility, offering new insights into the temporal control of gene expression in proliferating cells.
    Keywords:  (post-)transcriptional kinetics; CP: Molecular biology; cell cycle; chromatin accessibility dynamics; gene expression dynamics; mESCs; mRNA metabolism; single-cell multiomics; trajectory inference
    DOI:  https://doi.org/10.1016/j.celrep.2025.116089
  15. Cell Rep. 2025 Aug 06. pii: S2211-1247(25)00900-3. [Epub ahead of print]44(8): 116129
      Basic leucine zipper transcription factor ATF-like (BATF) plays a crucial role in CD8+ T cell (CTL) differentiation. Here, we demonstrated that BATF controls epigenomic and transcriptomic reprogramming of CTLs at the early stages of acute viral infection, thereby promoting effector CTL differentiation. Loss of BATF drastically perturbed gene expression, chromatin accessibility, and binding of key transcription factors. The BATF-interferon regulatory factor 4 (IRF4) interaction was essential for BATF-mediated effector differentiation, as the BATF mutant lacking this interaction failed to induce proper chromatin remodeling and proliferation of antigen-specific CTLs. Notably, IRF4 binding thoroughly depended on BATF, whereas BATF retained binding capacity even in IRF4-deficient CTLs. Furthermore, BATF initiated chromatin remodeling without IRF4; however, subsequent dynamic epigenomic reorganization required IRF4. These findings suggest that BATF serves as a "pioneer transcription factor" spearheading chromatin reorganization upon antigen encounter. This fundamental role is followed by further rearrangement of epigenomic and transcriptomic landscapes through the cooperation with IRF4.
    Keywords:  BATF; CD8(+) T cell differentiation; CP: Immunology; IRF4; chromatin landscape
    DOI:  https://doi.org/10.1016/j.celrep.2025.116129
  16. Cell. 2025 Jul 29. pii: S0092-8674(25)00803-7. [Epub ahead of print]
      Discrete genomic units can recombine into composite transposons that transcribe and transpose as single units, but their regulation and function are not fully understood. We report that composite transposons harbor bivalent histone marks, with activating and repressive marks in distinct regions. Genome-wide CRISPR-Cas9 screening, using a reporter driven by the hominid-specific composite transposon SVA (SINE [short interspersed nuclear element]-VNTR [variable number of tandem repeats]-Alu) in human cells, identified diverse genes that modify bivalent histone marks to regulate SVA transcription. SVA transcripts are critical for SVA's cis-regulatory function in selectively contacting and activating long-range gene expression. Remarkably, a subset of bivalent SVAs is activated during erythropoiesis to boost multiple erythroid gene expression, and knocking down these SVAs leads to deficient erythropoiesis. The RNA-dependent cis-regulatory function of SVA activates genes for myelopoiesis and can contribute to aging-associated myeloid-biased hematopoiesis. These results reveal that the cis-regulatory functions of composite transposons are bivalently regulated to control cell fate transitions in development and aging.
    Keywords:  RNA-dependent enhancer; SVA; aging; bivalent chromatin; cell fate transition; cis-regulatory elements; composite transposon; erythropoiesis; hematopoiesis; myelopoiesis
    DOI:  https://doi.org/10.1016/j.cell.2025.07.014
  17. Nat Commun. 2025 Aug 04. 16(1): 7138
      Bacterial σ factors bind RNA polymerase (E) to form holoenzyme (Eσ), conferring promoter specificity to E and playing a key role in transcription bubble formation. σN is unique among σ factors in its structure and functional mechanism, requiring activation by specialized AAA+ ATPases. EσN forms an inactive promoter complex where the N-terminal σN region I (σN-RI) threads through a small DNA bubble. On the opposite side of the DNA, the ATPase engages σN-RI within the pore of its hexameric ring. Here, we perform kinetics-guided structural analysis of de novo formed EσN initiation complexes and engineer a biochemical assay to measure ATPase-mediated σN-RI translocation during promoter melting. We show that the ATPase exerts mechanical action to translocate about 30 residues of σN-RI through the DNA bubble, disrupting inhibitory structures of σN to allow full transcription bubble formation. A local charge switch of σN-RI from positive to negative may help facilitate disengagement of the otherwise processive ATPase, allowing subsequent σN disentanglement from the DNA bubble.
    DOI:  https://doi.org/10.1038/s41467-025-61837-4
  18. Nat Commun. 2025 Aug 06. 16(1): 7248
      IRX3 is linked to predisposition to obesity through the FTO locus and is upregulated during early adipogenesis in risk-allele carriers, shifting adipocyte fate toward fat storage. However, how this elevated IRX3 expression influences later developmental stages remains unclear. Here we show that IRX3 regulates adipocyte fate by modulating epigenetic reprogramming. ChIP-sequencing in preadipocytes identifies over 300 IRX3 binding sites, predominantly at promoters of genes involved in SUMOylation and chromatin remodeling. IRX3 knockout alters expression of SUMO pathway genes, increases global SUMOylation, and inhibits PPARγ activity and adipogenesis. Pharmacological SUMOylation inhibition rescues these effects. IRX3 KO also reduces SUMO occupancy at Wnt-related genes, enhancing Wnt signaling and promoting osteogenic fate in 3D cultures. This fate switch is partially reversible by SUMOylation inhibition. We identify IRX3 as a key transcriptional regulator of epigenetic programs, acting upstream of SUMOylation to maintain mesenchymal identity and support adipogenesis while suppressing osteogenesis in mouse embryonic fibroblasts.
    DOI:  https://doi.org/10.1038/s41467-025-62361-1
  19. Dev Cell. 2025 Aug 01. pii: S1534-5807(25)00446-0. [Epub ahead of print]
      The nuclear lamina (NL), a perinuclear protein meshwork formed by nucleoskeleton and inner nuclear membrane (INM) proteins, is crucial for chromatin organization at the nuclear periphery and gene expression regulation in eukaryotic cells. However, NL-dependent transcriptional regulation remains poorly understood in plants due to the absence of most canonical NL proteins found in animals. Here, we report that the plant INM protein PLANT NUCLEAR ENVELOPE TRANSMEMBRANE 2 (PNET2) interacts with membrane-bound NAC (NAM, ATAF1/2, and CUC2) transcription factors, NTLs, via intrinsic disorder regions and promotes liquid-liquid phase separation within the NL. This compartmentalization effectively sequesters NTLs and restricts their transcriptional activity. In the absence of PNET2, NTLs become deregulated, triggering spontaneous and broad-spectrum stress responses. Importantly, we found that stress stimuli, such as heat shock, disrupt PNET2-NTL phase separation, releasing NTLs for target gene binding and transcriptional activation. These findings demonstrate a phase separation-based regulatory mechanism within the NL that controls membrane-bound transcription factor activity in response to environmental cues.
    Keywords:  NTL; PNET2; gene expression regulations; membrane-bound transcription factors; nuclear lamina; nuclear membrane; nucleoskeleton; phase separation; plant cells; stress responses
    DOI:  https://doi.org/10.1016/j.devcel.2025.07.008
  20. Nat Commun. 2025 Aug 07. 16(1): 7278
      Saccharomyces cerevisiae is closing-in on the first synthetic eukaryotic genome with genome-wide redesigns, including LoxPsym site insertions that enable inducible genomic rearrangements in vivo via Cre recombinase through SCRaMbLE (Synthetic Chromosome Recombination and Modification by LoxPsym-mediated Evolution). Combined with selection, SCRaMbLE quickly generates phenotype-enhanced strains by diversifying gene arrangement and content. Here, we demonstrate how iterative cycles of SCRaMbLE reorganises synthetic genome modules and chromosomes to improve functions. We introduce SCOUT (SCRaMbLE Continuous Output and Universal Tracker), a reporter system that allows sorting of SCRaMbLEd cells into high-diversity pools. Paired with long-read sequencing, SCOUT enables high-throughput mapping of genotype abundance and genotype-phenotype relationships. Iterative SCRaMbLE is applied here to yeast strains with a full synthetic chromosome and histidine biosynthesis modules. Five HIS module designs are tested, and SCRaMbLE is used to optimise the poorest performer. Our results highlight iterative SCRaMbLE as a powerful tool for data driven modular genome design.
    DOI:  https://doi.org/10.1038/s41467-025-62356-y
  21. BMC Bioinformatics. 2025 Aug 04. 26(1): 205
       BACKGROUND: Cellular development and differentiation in Eukaryotes depends upon sequential gene regulatory decisions that allow a single genome to encode many hundreds of distinct cellular phenotypes. Decisions are stored in the regulatory state of each cell, an important part of which is the epi-genome-the collection of proteins, RNA and their specific associations with the genome. Additionally, further cellular responses are, in part, determined by this regulatory state. To date, models of regulatory state have failed to include the contingency of incoming regulatory signals on the current epi-genetic state and none have done so at the whole-genome level.
    RESULTS: Here we introduce GenomicLayers, a new R package to run rules-based simulations of epigenetic state changes genome-wide in Eukaryotes. Simulations model the accumulation of changes to genome-wide layers by user-specified binding factors. As a first exemplar, we show two versions of a simple model of the recruitment and spreading of epigenetic marks near telomeres in the yeast Saccharomyces cerevisiae. By combining the output from 100 runs of the simulation, we generate whole genome predictions of epigenetic state at 1 bp resolution. The example yeast models are included within a 'vignette' with the GenomicLayers package, which is available at https://github.com/davetgerrard/GenomicLayers . To demonstrate the use of GenomicLayers on the full human reference genome (hg38), we show the results from parameter refinement on a simplistic model of the action of pluripotency factors against a self-spreading repressor seeded at CpG islands. The human genome model is included in supplementary information as an R script.
    CONCLUSIONS: GenomicLayers enables scientists working on diverse eukaryotic organisms to test models of gene regulation in silico. Applications include epigenetic silencing, activation by combinatorial binding of transcription factors and the sink effects caused by down-regulation of components of epigenetic regulators. The software is intended to be used to parameterise, refine and combine models and thereby capitalise on data from the thousands of studies of Eukaryotic epigenomes.
    Keywords:  Development; Epigenome; Genome; R; Simulation
    DOI:  https://doi.org/10.1186/s12859-025-06224-y
  22. Oncogene. 2025 Aug 04.
      Transcription factor (TF) fusion oncoproteins represent cancer-specific alterations that arise from chromosomal rearrangements. Through target gene recognition, TF fusions can disseminate transcriptional responses that collectively work to drive tumorigenesis. Thus, identifying the molecular targets that operate as a disease-driving network can potentially uncover key actionable dependencies. We have taken this strategy to dissect the underlying biological mechanism by which CIC::DUX4, a fusion oncoprotein associated with dismal outcomes, drives sarcomagenesis. We and others have defined a CIC::DUX4 fusion-mediated network that dysregulates cell-cycle and DNA replication checkpoints. Specifically, CIC::DUX4-mediated CCNE1 upregulation compromises the G1/S transition, leading to high DNA replication stress and conferring a dependence on the G2/M checkpoint kinase, WEE1. WEE1 provides a molecular brake to enable effective DNA repair prior to mitotic entry. Importantly, the mechanism by which CIC::DUX4 regulates DNA repair remains unknown. Here we show that the catalytic subunit of DNA polymerase epsilon (POLE) is essential for DNA integrity and cellular division in CIC::DUX4 sarcoma. Mechanistically, POLE loss increases DNA damage and induces p21-mediated cellular senescence to limit CIC::DUX4 tumor growth in vitro and tumor formation in vivo. Collectively, we credential POLE as a CIC::DUX4 target and further characterize a functional network through which CIC::DUX4 operates to drive tumor progression and survival.
    DOI:  https://doi.org/10.1038/s41388-025-03507-9
  23. Cell. 2025 Jul 29. pii: S0092-8674(25)00733-0. [Epub ahead of print]
      Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline, yet its epigenetic underpinnings remain elusive. Here, we generate and integrate single-cell epigenomic and transcriptomic profiles of 3.5 million cells from 384 postmortem brain samples across 6 regions in 111 AD and control individuals. We identify over 1 million candidate cis-regulatory elements (cCREs), organized into 123 regulatory modules across 67 cell subtypes. We define large-scale epigenomic compartments and single-cell epigenomic information and delineate their dynamics in AD, revealing widespread epigenome relaxation and brain-region-specific and cell-type-specific epigenomic erosion signatures during AD progression. These epigenomic stability dynamics are closely associated with cell-type proportion changes, glial cell-state transitions, and coordinated epigenomic and transcriptomic dysregulation linked to AD pathology, cognitive impairment, and cognitive resilience. This study provides critical insights into AD progression and cognitive resilience, presenting a comprehensive single-cell multiomic atlas to advance the understanding of AD.
    Keywords:  Alzheimer's disease; cognitive resilience; epigenomic erosion; epigenomic information; epigenomic stability; epigenomics; exhaustion; microglial activation; regulatory network; single-cell multiomics
    DOI:  https://doi.org/10.1016/j.cell.2025.06.031
  24. Genes Dev. 2025 Aug 06.
      We report here on the identification of a previously unrecognized property of MYOD as a repressor of gene expression via E-box-independent chromatin binding during the process of somatic cell trans-differentiation into skeletal muscle. When ectopically expressed in proliferating human fibroblasts or endogenously induced in activated muscle stem cells (MuSCs), MYOD was detected at accessible regulatory elements of expressed genes, invariably leading to reduced chromatin accessibility and gene repression. At variance with conventional E-box-driven increased chromatin accessibility and H3K27 acetylation at previously silent loci of MYOD-activated genes, MYOD-mediated chromatin compaction and repression of transcription was associated with high occurrence of non-E-box motifs and did not lead to reduced levels of H3K27ac but coincided with reduced levels of H4 acetyl-methyl lysine modification (Kacme). Using MYOD mutants, we dissected the molecular mechanism of MYOD-mediated repression, whereby repression of mitogen-responsive and growth factor-responsive genes occurred via promoter binding, which requires a conserved domain within the first helix; conversely, repression of cell of origin/alternative lineage genes occurred via binding and decommissioning of distal regulatory elements such as superenhancers (SEs), required either the N-terminal activation domain or the two chromatin remodeling domains, and coincided with reduced strength of CTCF-mediated chromatin interactions. These data extend MYOD biological properties beyond the current dogma that restricts MYOD function to a monotone transcriptional activator. They also reveal an unprecedented functional versatility arising from alternative chromatin recruitment through E-box or non-E-box sequences, whereby genetic determinants dictate differential usage of MYOD functional domains.
    Keywords:  MYOD; chromatin; gene expression
    DOI:  https://doi.org/10.1101/gad.352708.125
  25. Nature. 2025 Aug 06.
      NSD2 catalyses the epigenetic modification H3K36me2 (refs. 1,2) and is a candidate convergent downstream effector of oncogenic signalling in diverse malignancies3-5. However, it remains unclear whether the enzymatic activity of NSD2 is therapeutically targetable. Here we characterize a series of clinical-grade small-molecule catalytic NSD2 inhibitors (NSD2i) and show that the pharmacological targeting of NSD2 constitutes an epigenetic dependency with broad therapeutic efficacy in KRAS-driven preclinical cancer models. NSD2i inhibits NSD2 with single-digit nanomolar half-maximal inhibitory concentration potency and high selectivity over related methyltransferases. Structural analyses reveal that the specificity of NSD2i for NSD2 is due to competitive binding with S-adenosylmethionine and catalytic disruption through a binary-channel obstruction mechanism. Proteo-epigenomic and single-cell strategies in pancreatic and lung cancer models support a mechanism in which sustained NSD2i exposure reverses pathological H3K36me2-driven chromatin plasticity, re-establishing silencing at H3K27me3-legacy loci to curtail oncogenic gene expression programs. Accordingly, NSD2i impairs the viability of pancreatic and lung cancer cells and the growth of patient-derived xenograft tumours. Furthermore, NSD2i, which is well-tolerated in vivo, prolongs survival in advanced-stage autochthonous KRASG12C-driven pancreatic and lung tumours in mouse models to a comparable level as KRAS inhibition with sotorasib6. In these models, treatment with both a NSD2 inhibitor and sotorasib synergize to confer sustained survival with extensive tumour regression and elimination. Together, our work uncovers targeting of the NSD2-H3K36me2 axis as an actionable vulnerability in difficult to treat cancers and provides support for the evaluation of NSD2 and KRAS inhibitor combination therapies in a clinical setting.
    DOI:  https://doi.org/10.1038/s41586-025-09299-y
  26. Nat Genet. 2025 Aug 05.
      Genetic variants associated with major depressive disorder (MDD) are enriched in the regulatory genome. Here, we investigate gene-regulatory mechanisms underlying MDD compared to neurotypical controls by combining single-cell chromatin accessibility with gene expression in over 200,000 cells from the dorsolateral prefrontal cortex of 84 individuals. MDD-associated alterations in chromatin accessibility were prominent in deep-layer excitatory neurons characterized by transcription factor (TF) motif accessibility and binding of NR4A2, an activity-dependent TF reactive to stress. The same neurons were enriched for MDD-associated genetic variants, disrupting TF binding sites linked to genes that likely affect synaptic communication. Furthermore, a gray matter microglia cluster exhibited decreased accessibility in individuals with MDD at binding sites bound by TFs known to regulate immune homeostasis. Finally, we identified gene-regulatory effects of MDD-risk variants using sequence-based accessibility predictions, donor-specific genotypes and cell-based assays. These findings shed light on the cell types and regulatory mechanisms through which genetic variation may increase the risk of MDD.
    DOI:  https://doi.org/10.1038/s41588-025-02249-4
  27. Proc Natl Acad Sci U S A. 2025 Aug 12. 122(32): e2514190122
      DNA loop extrusion by cohesin has emerged as a critical pathway for chromosome organization. In vitro single-molecule experiments indicate that loop extrusion requires the assembly of a heteropentameric complex consisting of the SMC1/SMC3 heterodimer, STAG1, NIPBL, and the kleisin SCC1. The complexity of the complete extrusion machinery, consisting of multiple subunits, DNA binding sites, and ATPases poses substantial challenges for revealing the underlying biomolecular mechanism. As a result, a number of different models have been proposed, many of which do not agree on key mechanistic aspects, such as the details of DNA loading, holoenzyme assembly, or the consequences of ATP binding and hydrolysis. Here, we use mass photometry to comprehensively quantify all the key biomolecular interactions required for DNA loop extrusion. We find that STAG1 binds tightly to the trimeric complex formed by the SMC1/SMC3 heterodimer and SCC1, and together they weakly, but cooperatively, bind the DNA. Full-length NIPBL tightly binds DNA, acting as a DNA anchor during the mechanochemical loop extrusion cycle. Cohesin mutants incapable of head engagement, and those lacking DNA-binding domains in the ATPase heads show negligible differences in overall DNA-affinity, suggesting a minor role of these features for DNA binding. Instead, we find an ATP-modulated DNA binding site created by the interaction of STAG1 with SMC1/SMC3/SCC1, important for repeated grabbing and release of DNA critical to extrusion. Our results call for a careful reexamination of the proposed mechanisms and set energetic boundaries for future proposals.
    Keywords:  Cohesin; biomolecular mechanism; mass photometry; protein–protein interactions; single molecule
    DOI:  https://doi.org/10.1073/pnas.2514190122