bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2025–05–25
thirty-one papers selected by
Connor Rogerson, University of Cambridge
  1. Nucleosome dynamics render heterochromatin accessible in living human cells.
  2. U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation.
  3. Clonal tracing with somatic epimutations reveals dynamics of blood ageing.
  4. An Intrinsically Disordered Region of the FACT Subunit, Spt16, Promotes Chromatin Disassembly in Stimulating the Pre-Initiation Complex Formation at the Promoter for Transcription Initiation In Vivo.
  5. HBO1 functions as an epigenetic barrier to hepatocyte plasticity and reprogramming during liver injury.
  6. Restrictor slows RNAPII elongation to promote termination at noncoding RNA loci.
  7. Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing.
  8. Functional divergence of TBP homologs through distinct DNA-binding dynamics.
  9. CDX1 and CDX2 suppress colon cancer stemness by inhibiting β-catenin-facilitated formation of Pol II-DSIF-PAF1C complex.
  10. Deciphering the role of histone modifications in memory and exhausted CD8 T cells.
  11. Auricular malformations are driven by copy number variations in a hierarchical enhancer cluster and a dominant enhancer recapitulates human pathogenesis.
  12. CellWalker2: Multi-omic discovery using hierarchical cell type relationships.
  13. Global DNA methylation differences involving germline structural variation impact gene expression in pediatric brain tumors.
  14. Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12.
  15. Cell cycle-regulated transcriptional pausing of Drosophila replication-dependent histone genes.
  16. H3K4me3 binding ALFIN-LIKE proteins recruit SWR1 for gene-body deposition of H2A.Z.
  17. A specific form of cPRC1 containing CBX4 is co-opted to mediate oncogenic gene repression in diffuse midline glioma.
  18. Comprehensive evaluation of phosphoproteomic-based kinase activity inference.
  19. The SAMD1 transcription factor coordinates hematopoietic lineage differentiation and H3K4 methylation status.
  20. Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits.
  21. Sequential activation of transcription factors promotes liver regeneration through specific and developmental enhancers.
  22. Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity.
  23. A single high-zinc activation enhancer can control two genes oriented head-to-head in Caenorhabditis elegans.
  24. DEK-nucleosome structure shows DEK modulates H3K27me3 and stem cell fate.
  25. MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures.
  26. The ALX4 dimer structure provides insight into how disease alleles impact function.
  27. DNA replication timing reveals genome-wide features of transcription and fragility.
  28. Integrative characterization of MYC RNA-binding function.
  29. RobusTAD: reference panel based annotation of nested topologically associating domains.
  30. CREATE: cell-type-specific cis-regulatory element identification via discrete embedding.
  31. Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise.
  1. Nat Commun. 2025 May 16. 16(1): 4577
    Nucleosome dynamics render heterochromatin accessible in living human cells.
    Hemant K Prajapati, Zhuwei Xu, Peter R Eriksson, David J Clark.
      The eukaryotic genome is packaged into chromatin, which is composed of a nucleosomal filament that coils up to form more compact structures. Chromatin exists in two main forms: euchromatin, which is relatively decondensed and enriched in transcriptionally active genes, and heterochromatin, which is condensed and transcriptionally repressed. It is widely accepted that chromatin architecture modulates DNA accessibility, restricting the access of sequence-specific, gene-regulatory, transcription factors to the genome. However, the evidence for this model derives primarily from experiments with isolated nuclei, in which chromatin remodeling has ceased, resulting in a static chromatin structure. Here, using a DNA methyltransferase to measure accessibility in vivo, we show that both euchromatin and heterochromatin are fully accessible in living human cells, whereas centromeric α-satellite chromatin is partly inaccessible. We conclude that all nucleosomes in euchromatin and heterochromatin are highly dynamic in living cells, except for nucleosomes in centromeric chromatin.
    DOI:  https://doi.org/10.1038/s41467-025-59994-7
  2. Mol Cell. 2025 May 15. pii: S1097-2765(25)00363-6. [Epub ahead of print]85(10): 1968-1981.e7
    U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation.
    GyeungYun Kim, Christine L Carroll, Zachary Peters Wakefield, Mustafa Tuncay, Ana Fiszbein.
      Emerging evidence indicates that splicing factors mediate the close link between transcription and splicing. However, the mechanisms underlying this coupling remain unclear. U1 small nuclear ribonucleoprotein particle (U1 snRNP) not only initiates splicing but also plays a crucial role in preventing premature cleavage and polyadenylation, facilitating long-distance transcriptional elongation. Here, we show that U1 snRNP regulates alternative promoter activity in human cells by inhibiting premature polyadenylation. In genes carrying premature polyadenylation sites between two promoters, U1 snRNP inhibition with antisense oligonucleotides leads to a significant decrease in downstream promoter activity. Conversely, restoring U1 snRNP activity or inhibiting premature polyadenylation rescues downstream promoter activity. Mechanistically, U1 snRNP inhibition correlates with reduced chromatin accessibility, decreased RNA polymerase II serine 5 phosphorylation, and increased promoter-proximal pause at downstream promoters. Our findings support a model in which U1 snRNP favors productive elongation from upstream promoters, triggering downstream promoter activation by destabilizing nucleosomes and promoting promoter escape.
    Keywords:  U1 snRNP; alternative promoters; dowsntream promoters; promoter-proximal pause; splicing factors; splicing transcription; transcription cooperativity; transcription initiation; transcription interfierence; transcription start sites
    DOI:  https://doi.org/10.1016/j.molcel.2025.04.021
  3. Nature. 2025 May 21.
    Clonal tracing with somatic epimutations reveals dynamics of blood ageing.
    Michael Scherer, Indranil Singh, Martina Maria Braun, Chelsea Szu-Tu, Pedro Sanchez Sanchez, Dominik Lindenhofer, Niels Asger Jakobsen, Verena Körber, Michael Kardorff, Lena Nitsch, Pauline Kautz, Julia Rühle, Agostina Bianchi, Luca Cozzuto, Robert Frömel, Sergi Beneyto-Calabuig, Caleb Lareau, Ansuman T Satpathy, Renée Beekman, Lars M Steinmetz, Simon Raffel, Leif S Ludwig, Paresh Vyas, Alejo Rodriguez-Fraticelli, Lars Velten.
      Current approaches used to track stem cell clones through differentiation require genetic engineering1,2 or rely on sparse somatic DNA variants3,4, which limits their wide application. Here we discover that DNA methylation of a subset of CpG sites reflects cellular differentiation, whereas another subset undergoes stochastic epimutations and can serve as digital barcodes of clonal identity. We demonstrate that targeted single-cell profiling of DNA methylation5 at single-CpG resolution can accurately extract both layers of information. To that end, we develop EPI-Clone, a method for transgene-free lineage tracing at scale. Applied to mouse and human haematopoiesis, we capture hundreds of clonal differentiation trajectories across tens of individuals and 230,358 single cells. In mouse ageing, we demonstrate that myeloid bias and low output of old haematopoietic stem cells6 are restricted to a small number of expanded clones, whereas many functionally young-like clones persist in old age. In human ageing, clones with and without known driver mutations of clonal haematopoieis7 are part of a spectrum of age-related clonal expansions that display similar lineage biases. EPI-Clone enables accurate and transgene-free single-cell lineage tracing on hematopoietic cell state landscapes at scale.
    DOI:  https://doi.org/10.1038/s41586-025-09041-8
  4. Mol Cell Biol. 2025 May 23. 1-20
    An Intrinsically Disordered Region of the FACT Subunit, Spt16, Promotes Chromatin Disassembly in Stimulating the Pre-Initiation Complex Formation at the Promoter for Transcription Initiation In Vivo.
    Priyanka Barman, Sukesh R Bhaumik.
      Previous structural and biochemical studies revealed that a negatively charged intrinsically disordered region (IDR) at the C-terminal of the Spt16 subunit of an evolutionarily conserved heterodimeric histone chaperone, FACT (Facilitates chromatin transcription), interacts with histone H2A-H2B dimer, and hence interferes the interaction of DNA with histone H2A-H2B dimer. However, the functional relevance of the binding of Spt16's IDR to histone H2A-H2B dimer with impact on chromatin dynamics and transcription has not been clearly elucidated in living cells. Here, we show that Spt16's IDR facilitates the eviction of histone H2A-H2B dimer (and hence chromatin disassembly) from the inducible GAL promoters upon transcription induction. Such facilitation of chromatin disassembly by Spt16's IDR stimulates the pre-initiation complex (PIC) formation at the promoter, and hence transcription initiation. Further, we find that Spt16's IDR regulates chromatin reassembly at the coding sequence in the wake of elongating RNA polymerase II. Collectively, our results reveal that Spt16's IDR facilitates promoter chromatin disassembly for stimulation of the PIC formation for transcription initiation with additional function in chromatin reassembly at the coding sequence in the wake of elongating RNA polymerase II, thus illuminating novel IDR regulation of chromatin dynamics and transcription in vivo.
    Keywords:  Chromatin; Spt16; TBP and RNA polymerase II; Transcription
    DOI:  https://doi.org/10.1080/10985549.2025.2501630
  5. Cell Stem Cell. 2025 May 19. pii: S1934-5909(25)00177-8. [Epub ahead of print]
    HBO1 functions as an epigenetic barrier to hepatocyte plasticity and reprogramming during liver injury.
    Wei-Chien Yuan, Andrew S Earl, Sai Ma, Karel Alcedo, Jacquelyn O Russell, Fabiana M Duarte, Yen-Ting Chu, Pei-Chi Chang, Hsin-Yi Chen, Hsin-Hui Chi, Qian Zhu, Alejo E Rodriguez-Fraticelli, Sachin H Patel, Yu-Ru Lee, Jason D Buenrostro, Fernando D Camargo.
      Hepatocytes can reprogram into biliary epithelial cells (BECs) during liver injury, but the underlying epigenetic mechanisms remain poorly understood. Here, we define the chromatin dynamics of this process using single-cell ATAC-seq and identify YAP/TEAD activation as a key driver of chromatin remodeling. An in vivo CRISPR screen highlights the histone acetyltransferase HBO1 as a critical barrier to reprogramming. HBO1 is recruited by YAP to target loci, where it promotes histone H3 lysine 14 acetylation (H3K14ac) and engages the chromatin reader zinc-finger MYND-type containing 8 (ZMYND8) to suppress YAP/TEAD-driven transcription. Loss of HBO1 accelerates chromatin remodeling, enhances YAP binding, and enables a more complete hepatocyte-to-BEC transition. Our findings position HBO1 as an epigenetic brake that restrains YAP-mediated reprogramming, suggesting that targeting HBO1 may enhance hepatocyte plasticity for liver regeneration.
    Keywords:  HBO1; Hippo-YAP; epigenetic regulation; hepatocyte reprogramming; in vivo CRISPR screen
    DOI:  https://doi.org/10.1016/j.stem.2025.04.010
  6. Genes Dev. 2025 May 20.
    Restrictor slows RNAPII elongation to promote termination at noncoding RNA loci.
    Claudia A Mimoso, Hanneke Vlaming, Nathalie P de Wagenaar, Allison P Siegenfeld, Karen Adelman.
      The eukaryotic genome is broadly transcribed by RNA polymerase II (RNAPII) to produce protein-coding messenger RNAs (mRNAs) and a repertoire of noncoding RNAs (ncRNAs). Although RNAPII is very processive during mRNA transcription, it terminates rapidly during synthesis of many ncRNAs, particularly those that arise opportunistically from accessible chromatin at gene promoters or enhancers. The divergent fates of mRNA versus ncRNA species raise many questions about how RNAPII and associated machineries discriminate functional from spurious transcription. Restrictor, comprised of the RNA binding protein ZC3H4 and RNAPII-interacting protein WDR82, has been implicated in restraining the expression of ncRNAs. However, the determinants of Restrictor specificity and the mechanism of transcription suppression remain unclear. Here, we investigate Restrictor using unbiased sequence screens and rapid protein degradation followed by nascent RNA sequencing. We found that Restrictor promiscuously suppresses early elongation by RNAPII, but this activity is blocked at most mRNAs by the presence of a 5' splice site. Consequently, Restrictor is a critical determinant of transcription directionality at divergent promoters and prevents transcriptional interference. Mechanistically, we show that rather than terminating RNAPII directly, Restrictor acts by reducing the rate of transcription elongation, rendering RNAPII susceptible to early termination by other machineries.
    Keywords:  RNA processing; U1 snRNP; elongation; high-throughput sequence screen; noncoding RNA; transcription; transcription termination
    DOI:  https://doi.org/10.1101/gad.352654.125
  7. Cell Rep Methods. 2025 May 15. pii: S2667-2375(25)00088-8. [Epub ahead of print] 101052
    Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing.
    Alexi Tallan, Jack Kucinski, Benjamin Sunkel, Cenny Taslim, Stephanie LaHaye, Qi Liu, Jun Qi, Meng Wang, Genevieve C Kendall, Benjamin Z Stanton.
      Quantitative comparison of ChIP-seq profiling between experimental conditions or samples remains technically challenging for the epigenetics field. Here, we report a strategy combining the use of well-defined cellular spike-in ratios of orthologous species' chromatin and a bioinformatic analysis pipeline to facilitate highly quantitative comparisons of 2D chromatin sequencing across experimental conditions. We find that the PerCell methodology results in efficient and consistent levels of spike-in vs. experimental genomic reads. We demonstrate use of the method and pipeline to enable quantitative, internally normalized chromatin sequencing on zebrafish embryos and human cancer cells. Overall, we propose the PerCell method to enable cross-species comparative epigenomics and promote uniformity of data analyses and sharing across labs.
    Keywords:  CP: molecular biology; CP: systems biology; Nextflow; chromatin sequencing; cross-species epigenomics; genomics normalization; quantitative epigenomics; sarcoma; transcription factor
    DOI:  https://doi.org/10.1016/j.crmeth.2025.101052
  8. Nucleic Acids Res. 2025 May 10. pii: gkaf436. [Epub ahead of print]53(9):
    Functional divergence of TBP homologs through distinct DNA-binding dynamics.
    Jieying H Cui, James Z J Kwan, Armin Faghihi, Thomas F Nguyen, Sheila S Teves.
      The TATA box-binding protein (TBP) is an evolutionarily conserved basal transcription factor common in the pre-initiation complex of all three eukaryotic RNA polymerases (RNA Pols). Despite their high conservation, homologous TBPs exhibit species- and tissue-specific functions that may contribute to the increasingly complex gene expression regulation across evolutionary time. To determine the molecular mechanisms of species- and tissue-specificity for homologous TBPs, we examined the ability of yeast TBP and murine TBP paralogs to replace the endogenous TBP in mouse embryonic stem cells (mESCs). We show that, despite the high conservation in the DNA-binding domain among the homologs, they cannot fully rescue the lethality of TBP depletion in mESCs, which correlates with their inability to support RNA Pol III transcription. Furthermore, we show that the homologs differentially support stress-induced transcription reprogramming, with the divergent N-terminal domain playing a role in modulating changes in transcriptional response. Lastly, we show that the homologs have vastly different DNA binding dynamics, suggesting a potential mechanism for the distinct functional behavior observed among the homologs. Taken together, these data show a remarkable balance between flexibility and essentiality for the different functions of homologous TBP in eukaryotic transcription.
    DOI:  https://doi.org/10.1093/nar/gkaf436
  9. Cell Death Dis. 2025 May 21. 16(1): 408
    CDX1 and CDX2 suppress colon cancer stemness by inhibiting β-catenin-facilitated formation of Pol II-DSIF-PAF1C complex.
    Koji Aoki, Akari Nitta, Ayumi Igarashi.
      Homeobox transcription factors CDX1 and CDX2 (hereafter, CDX1/2) play key roles in determining the identity of intestinal epithelial cells and regulating their stem cell functions. However, the role of CDX1/2 in regulating colon cancer stemness and the underlying mechanisms are unclear. Here, we show that complete loss of Cdx1 or concurrent loss of Cdx1/2 increased the stemness and malignancy of intestinal tumors. Consistently, CDX1/2 reduced the expression of cancer stemness-related genes, including LGR5. CDX1/2 bound to the downstream region of the LGR5 transcription start site (TSS), a region where β-catenin also binds. Despite increased H3 acetylation and an open chromatin structure, CDX1/2 reduced the occupancy of DRB sensitivity-inducing factor (DSIF), RNA polymerase II-associated factor 1 (PAF1), and RNA polymerase II (Pol II) complexes around the LGR5 TSS. Through their homeodomains, CDX1/2 inhibited the β-catenin-facilitated formation of active Pol II complexes containing DSIF and PAF1 complexes by preventing the interaction between β-catenin and these complexes, in an additive manner. Our findings suggest that CDX1/2 cooperatively suppressed colonic tumorigenesis and cancer stemness by antagonizing β-catenin via the DSIF and PAF1 complexes. Additionally, DSIF and PAF1 complexes acted as transcriptional platforms that integrated and funneled both tumor-suppressive and oncogenic signals into the expression of genes that control colon cancer stemness.
    DOI:  https://doi.org/10.1038/s41419-025-07737-3
  10. Sci Rep. 2025 May 19. 15(1): 17359
    Deciphering the role of histone modifications in memory and exhausted CD8 T cells.
    Hua Huang, Amy E Baxter, Zhen Zhang, Charly R Good, Katherine A Alexander, Zeyu Chen, Paula A Agudelo Garcia, Parisa Samareh, Sierra M Collins, Karl M Glastad, Lu Wang, Gregory Donahue, Sasikanth Manne, Josephine R Giles, Junwei Shi, Shelley L Berger, E John Wherry.
      Exhausted CD8 T cells (TEX) arising during chronic infections and cancer have reduced functional capacity and limited fate flexibility that prevents optimal disease control and response to immunotherapies. Compared to memory (TMEM) cells, TEX have a unique open chromatin landscape underlying a distinct gene expression program. How TEX transcriptional and epigenetic landscapes are regulated through histone post-translational modifications (hPTMs) remains unclear. Here, we profiled key activating (H3K27ac and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in naive CD8 T cells (TN), TMEM and TEX. We identified H3K27ac-associated super-enhancers that distinguish TN, TMEM and TEX, along with key transcription factor networks predicted to regulate these different transcriptional landscapes. Promoters of some key genes were poised in TN, but activated in TMEM or TEX whereas other genes poised in TN were repressed in TMEM or TEX, indicating that both repression and activation of poised genes may enforce these distinct cell states. Moreover, narrow peaks of repressive H3K9me3 were associated with increased gene expression in TEX, suggesting an atypical role for this modification. These data indicate that beyond chromatin accessibility, hPTMs differentially regulate specific gene expression programs of TEX compared to TMEM through both activating and repressive pathways.
    DOI:  https://doi.org/10.1038/s41598-025-99804-0
  11. Nat Commun. 2025 May 17. 16(1): 4598
    Auricular malformations are driven by copy number variations in a hierarchical enhancer cluster and a dominant enhancer recapitulates human pathogenesis.
    Xiaopeng Xu, Qi Chen, Qingpei Huang, Timothy C Cox, Hao Zhu, Jintian Hu, Xi Han, Ziqiu Meng, Bingqing Wang, Zhiying Liao, Wenxin Xu, Baichuan Xiao, Ruirui Lang, Jiqiang Liu, Jian Huang, Xiaokai Tang, Jinmo Wang, Qiang Li, Ting Liu, Qingguo Zhang, Stylianos E Antonarakis, Jiao Zhang, Xiaoying Fan, Huisheng Liu, Yong-Biao Zhang.
      Enhancers, through the combinatorial action of transcription factors (TFs), dictate both the spatial specificity and the levels of gene expression, and their aberrations can result in diseases. While a HMX1 downstream enhancer is associated with ear malformations, the mechanisms underlying bilateral constricted ear (BCE) remain unclear. Here, we identify a copy number variation (CNV) containing three enhancers-collectively termed the positional identity hierarchical enhancer cluster (PI-HEC)-that drives BCE by coordinately regulating HMX1 expression. Each enhancer exhibits distinct activity-location-structure features, and the dominant enhancer with high mobility group (HMG)-box combined with Coordinator and homeodomain TF motifs modulating its activity and specificity, respectively. Mouse models demonstrate that neural crest-derived fibroblasts with aberrant Hmx1 expression in the basal pinna, along with ectopic distal pinna expression, disrupt outer ear development, affecting cartilage, muscle, and epidermis. Our findings elucidate mammalian ear morphogenesis and underscore the complexity of synergistic regulation among enhancers and between enhancers and transcription factors.
    DOI:  https://doi.org/10.1038/s41467-025-59735-w
  12. Cell Genom. 2025 May 20. pii: S2666-979X(25)00142-9. [Epub ahead of print] 100886
    CellWalker2: Multi-omic discovery using hierarchical cell type relationships.
    Zhirui Hu, Pawel F Przytycki, Katherine S Pollard.
      Tissues are composed of cells with a wide range of similarities to each other, yet existing methods for single-cell genomics treat cell types as discrete labels. To address this gap, we developed CellWalker2, a graph diffusion-based model for the annotation and mapping of multi-modal data. With our open-source software package, hierarchically related cell types can be probabilistically matched across contexts and used to annotate cells, genomic regions, or gene sets. Additional features include estimating statistical significance and enabling gene expression and chromatin accessibility to be jointly modeled. Through simulation studies, we show that CellWalker2 performs better than existing methods in cell-type annotation and mapping. We then use multi-omics data from the brain and immune system to demonstrate CellWalker2's ability to assign high-resolution cell-type labels to regulatory elements and TFs and to quantify both conserved and divergent cell-type relationships between species.
    Keywords:  cell type; comparative genomics; gene regulation; graph; hierarchical; multi-omics; single cell; transcription factors
    DOI:  https://doi.org/10.1016/j.xgen.2025.100886
  13. Nat Commun. 2025 May 21. 16(1): 4713
    Global DNA methylation differences involving germline structural variation impact gene expression in pediatric brain tumors.
    Fengju Chen, Yiqun Zhang, Wei Li, Fritz J Sedlazeck, Lanlan Shen, Chad J Creighton.
      The extent of genetic variation and its influence on gene expression across multiple tissue and cellular contexts is still being characterized, with germline Structural Variants (SVs) being historically understudied. DNA methylation also represents a component of normal germline variation across individuals. Here, we combine germline SVs (by short-read sequencing) with tumor DNA methylation across 1292 pediatric brain tumor patients. For thousands of methylation probes for CpG Islands (CGIs) or enhancers, rare and common SV breakpoints upstream or downstream associate with differential methylation in tumors spanning various histologic types, a significant subset involving genes with SV-associated differential expression. Cancer predisposition genes involving SV-associated differential methylation and expression include MSH2, RSPA, and PALB2. SV breakpoints falling within CGIs or histone marks H3K36me3 or H3K9me3 associate with differential CGI methylation. Genes with SVs and CGI methylation associated with patient survival include POLD4. Our results capture a class of normal phenotypic variation having disease implications.
    DOI:  https://doi.org/10.1038/s41467-025-60110-y
  14. Nat Commun. 2025 May 19. 16(1): 4656
    Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12.
    Selina Troester, Thomas Eder, Nadja Wukowits, Martin Piontek, Pablo Fernández-Pernas, Johannes Schmoellerl, Ben Haladik, Gabriele Manhart, Melanie Allram, Margarita Maurer-Granofszky, Nastassja Scheidegger, Karin Nebral, Giulio Superti-Furga, Roland Meisel, Beat Bornhauser, Peter Valent, Michael N Dworzak, Johannes Zuber, Kaan Boztug, Florian Grebien.
      Nucleoporin 98 (NUP98) fusion oncoproteins are strong drivers of pediatric acute myeloid leukemia (AML) with poor prognosis. Here we show that NUP98 fusion-expressing AML harbors an epigenetic signature that is characterized by increased accessibility of hematopoietic stem cell genes and enrichment of activating histone marks. We employ an AML model for ligand-induced degradation of the NUP98::KDM5A fusion oncoprotein to identify epigenetic programs and transcriptional targets that are directly regulated by NUP98::KDM5A through CUT&Tag and nascent RNA-seq. Orthogonal genome-wide CRISPR/Cas9 screening identifies 12 direct NUP98::KDM5A target genes, which are essential for AML cell growth. Among these, we validate cyclin-dependent kinase 12 (CDK12) as a druggable vulnerability in NUP98::KDM5A-expressing AML. In line with its role in the transcription of DNA damage repair genes, small-molecule-mediated CDK12 inactivation causes increased DNA damage, leading to AML cell death. Altogether, we show that NUP98::KDM5A directly regulates a core set of essential target genes and reveal CDK12 as an actionable vulnerability in AML with oncogenic NUP98 fusions.
    DOI:  https://doi.org/10.1038/s41467-025-59930-9
  15. Mol Biol Cell. 2025 May 21. mbcE25050212
    Cell cycle-regulated transcriptional pausing of Drosophila replication-dependent histone genes.
    James P Kemp, Mark S Geisler, Mia Hoover, Chun-Yi Cho, Patrick H O'Farrell, William F Marzluff, Robert J Duronio.
      Coordinated expression of replication-dependent (RD) histones genes occurs within the Histone Locus Body (HLB) during S phase, but the molecular steps in transcription that are cell cycle regulated are unknown. We report that Drosophila RNA Pol II promotes HLB formation and is enriched in the HLB outside of S phase, including G1-arrested cells that do not transcribe RD histone genes. In contrast, the transcription elongation factor Spt6 is enriched in HLBs only during S phase. Proliferating cells in the wing and eye primordium express full-length histone mRNAs during S phase but express only short nascent transcripts in cells in G1 or G2 consistent with these transcripts being paused and then terminated. Full-length transcripts are produced when Cyclin E/Cdk2 is activated as cells enter S phase. Thus, activation of transcription elongation by Cyclin E/Cdk2 and not recruitment of RNA pol II to the HLB is the critical step that links histone gene expression to cell cycle progression. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text].
    DOI:  https://doi.org/10.1091/mbc.E25-05-0212
  16. Genome Biol. 2025 May 21. 26(1): 137
    H3K4me3 binding ALFIN-LIKE proteins recruit SWR1 for gene-body deposition of H2A.Z.
    Linhao Xu, Yafei Wang, Xueying Li, Qin Hu, Vanda Adamkova, Junjie Xu, C Jake Harris, Israel Ausin.
       BACKGROUND: The H2A.Z histone variant is highly enriched over gene bodies, playing an essential role in several genome-templated processes, including transcriptional regulation and epigenetic patterning across eukaryotes. Deposition of H2A.Z is mediated by the SWR1 remodeling complex. How SWR1 is directed to gene bodies is largely unknown.
    RESULTS: Here, we show that ALFIN-LIKE (AL) proteins are responsible for H2A.Z gene body patterning in Arabidopsis. AL proteins encode H3K4me3-binding PHD domains, and by ChIP-seq, we confirm preferential binding of AL5 to H3K4me3 over H3K4me1/2 in planta. We observe a global reduction in H2A.Z in al septuple mutants (al7m), especially over H3K4me3-enriched genic regions. While MBD9 recruits SWR1 to nucleosome-free regions, ALs act non-redundantly with MBD9 for deposition of H2A.Z. Notably, al7m mutants show severe developmental abnormalities and upregulation of H2A.Z gene body-enriched responsive genes.
    CONCLUSIONS: Therefore, we propose a model whereby AL proteins direct gene body enrichment of H2A.Z by recruiting SWR1 to H3K4me3-containing responsive genes.
    DOI:  https://doi.org/10.1186/s13059-025-03605-7
  17. Mol Cell. 2025 May 21. pii: S1097-2765(25)00405-8. [Epub ahead of print]
    A specific form of cPRC1 containing CBX4 is co-opted to mediate oncogenic gene repression in diffuse midline glioma.
    Eimear Lagan, Dáire Gannon, Ademar Jesus Silva, Peter Bibawi, Anthony M Doherty, Darragh Nimmo, Rachel McCole, Craig Monger, Giovani Luiz Genesi, Aurelie Vanderlinden, James A Innes, Charlotte L E Jones, Lu Yang, Bryan Chen, Guido van Mierlo, Pascal W T C Jansen, Chinmayi Pednekar, Alexander Von Kriegsheim, Kieran Wynne, Francisco J Sánchez-Rivera, Yadira M Soto-Feliciano, Angel M Carcaboso, Michiel Vermeulen, Giorgio Oliviero, Chun-Wei Chen, Richard E Phillips, Adrian P Bracken, Gerard L Brien.
      Diffuse midline glioma (DMG) is a fatal childhood brain tumor characterized primarily by mutant histone H3 (H3K27M). H3K27M causes a global reduction in Polycomb repressive complex 2 (PRC2)-mediated H3K27 trimethylation (H3K27me3). Paradoxically, PRC2 is essential in DMG cells, although the downstream molecular mechanisms are poorly understood. Here, we have discovered a specific form of canonical PRC1 (cPRC1) containing CBX4 and PCGF4 that drives oncogenic gene repression downstream of H3K27me3 in DMG cells. Via a novel functional region, CBX4 preferentially associates with PCGF4-containing cPRC1. The characteristic H3K27me3 landscape in DMG rewires the distribution of cPRC1 complexes, with CBX4/PCGF4-cPRC1 accumulating at H3K27me3-enriched CpG islands. Despite comprising <5% of cPRC1 in DMG cells, the unique repressive functions of CBX4/PCGF4-cPRC1 are essential for DMG growth. Our findings link the altered distribution of H3K27me3 to imbalanced cPRC1 function, which drives oncogenic gene repression in DMG, highlighting potential therapeutic opportunities for this incurable childhood brain cancer.
    Keywords:  CBX4; EZH2; H3K27M; H3K27me3; PCGF4; PRC1; PRC2; Polycomb; diffuse intrinic pontine glioma; diffuse midline glioma
    DOI:  https://doi.org/10.1016/j.molcel.2025.04.026
  18. Nat Commun. 2025 May 22. 16(1): 4771
    Comprehensive evaluation of phosphoproteomic-based kinase activity inference.
    Sophia Müller-Dott, Eric J Jaehnig, Khoi Pham Munchic, Wen Jiang, Tomer M Yaron-Barir, Sara R Savage, Martin Garrido-Rodriguez, Jared L Johnson, Alessandro Lussana, Evangelia Petsalaki, Jonathan T Lei, Aurelien Dugourd, Karsten Krug, Lewis C Cantley, D R Mani, Bing Zhang, Julio Saez-Rodriguez.
      Kinases regulate cellular processes and are essential for understanding cellular function and disease. To investigate the regulatory state of a kinase, numerous methods have been developed to infer kinase activities from phosphoproteomics data using kinase-substrate libraries. However, few phosphorylation sites can be attributed to an upstream kinase in these libraries, limiting the scope of kinase activity inference. Moreover, inferred activities vary across methods, necessitating evaluation for accurate interpretation. Here, we present benchmarKIN, an R package enabling comprehensive evaluation of kinase activity inference methods. Alongside classical perturbation experiments, benchmarKIN introduces a tumor-based benchmarking approach utilizing multi-omics data to identify highly active or inactive kinases. We used benchmarKIN to evaluate kinase-substrate libraries, inference algorithms and the potential of adding predicted kinase-substrate interactions to overcome the coverage limitations. Our evaluation shows most computational methods perform similarly, but the choice of library impacts the inferred activities with a combination of manually curated libraries demonstrating superior performance in recapitulating kinase activities. Additionally, in the tumor-based evaluation, adding predicted targets from NetworKIN further boosts the performance. We then demonstrate how kinase activity inference aids characterize kinase inhibitor responses in cell lines. Overall, benchmarKIN helps researchers to select reliable methods for identifying deregulated kinases.
    DOI:  https://doi.org/10.1038/s41467-025-59779-y
  19. Blood Adv. 2025 May 22. pii: bloodadvances.2024015627. [Epub ahead of print]
    The SAMD1 transcription factor coordinates hematopoietic lineage differentiation and H3K4 methylation status.
    Meg A Schaefer, Samantha L Gomez, Venkatasai Rahul Dogiparthi, Yichao J Zhou, Pooja Roy, Suhita J Ray, Linda Chee, Sandipan Brahma, Robert Liefke, Kyle J Hewitt.
      Cell progenitor to progeny transitions depend on precise transcriptional mechanisms to adjust gene expression. The sterile alpha motif-containing 1 protein (SAMD1) regulates a shift in transcriptional activity during embryonic stem cell exit from pluripotency. SAMD1 interacts with and facilitates the activity of the histone H3 lysine demethylating enzyme LSD1. SAMD1 is expressed throughout many biological systems, but its role in hematopoiesis is unknown. In human and mouse hematopoietic stem/progenitor cells, we tested the role of SAMD1 in hematopoiesis and erythropoiesis using loss-of-function approaches. SAMD1 promoted expression of critical drivers of hematopoiesis, including the GATA2 transcription factor, while opposing erythroid programs. Loss of SAMD1 in ex vivo differentiating cells increased erythroid and megakaryocyte differentiation and altered the landscape of histone H3K4 methylation genome-wide. Cohorts of SAMD1-repressed genes are linked to erythropoietic activities. SAMD1 expression promoted ERK signaling via SCF/Kit stimulation in progenitor populations. In erythroid precursor cells, SAMD1 co-occupies chromatin with LSD1 and GATA factors. Whereas SAMD1 downregulates H3K4me2 levels genome-wide, contributing to gene repression, SAMD1 also elevates transcription at select sites. To test Samd1 function in hematopoiesis, we performed competitive transplant experiments in mice. Samd1 knockdown hematopoietic stem cells (HSCs) contributed more to peripheral blood mononuclear cells versus control HSCs. Our results establish SAMD1 as a coordinator of H3K4 methylation and stem/progenitor activity in hematopoiesis and erythropoiesis.
    DOI:  https://doi.org/10.1182/bloodadvances.2024015627
  20. Genome Res. 2025 May 20. pii: gr.279741.124. [Epub ahead of print]
    Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits.
    Kevin W Currin, Hannah J Perrin, Gautam K Pandey, Abdalla A Alkhawaja, Swarooparani Vadlamudi, Annie E Musser, Amy S Etheridge, K Alaine Broadaway, Jonathan D Rosen, Arushi Varshney, Amarjit S Chaudhry, Paul J Gallins, Fred A Wright, Yi-Hui Zhou, Stephen Cj Parker, Laura M Raffield, Erin G Schuetz, Federico Innocenti, Karen L Mohlke.
      Chromatin accessibility quantitative trait locus (caQTL) studies have identified regulatory elements that underlie genetic effects on gene expression and metabolic traits. However, caQTL discovery has been limited by small sample sizes. Here, we mapped caQTLs in liver tissue from 138 human donors and identified caQTLs for 35,361 regulatory elements, including population-specific caQTLs driven by differences in allele frequency across populations. We identified 2,126 genetic signals associated with multiple, presumably coordinately regulated elements. Coordinately regulated elements linked distal elements to target genes and were more likely to be associated with gene expression compared to single-element caQTLs. We predicted driver and response elements at coordinated loci and found that driver elements were enriched for transcription factor binding sites of key liver regulators. We identified colocalized caQTLs at 667 genome-wide association (GWAS) signals for metabolic and liver traits and annotated these loci with predicted target genes and disrupted transcription factor binding sites. CaQTLs identified three-fold more GWAS colocalizations than liver expression QTLs (eQTLs) in a larger sample size, suggesting that caQTLs can detect mechanisms missed by eQTLs. At a GWAS signal colocalized with a caQTL and an eQTL for TENM2, we validated regulatory activity for a variant within a predicted driver element that was coordinately regulated with 39 other elements. At another locus, we validated a predicted enhancer of RALGPS2 using CRISPR interference and demonstrated allelic effects on transcription for a haplotype within this enhancer. These results demonstrate the power of caQTLs to characterize regulatory mechanisms at GWAS loci.
    DOI:  https://doi.org/10.1101/gr.279741.124
  21. Cell Genom. 2025 May 20. pii: S2666-979X(25)00143-0. [Epub ahead of print] 100887
    Sequential activation of transcription factors promotes liver regeneration through specific and developmental enhancers.
    Palmira Llorens-Giralt, Marina Ruiz-Romero, Ramil Nurtdinov, Macarena Herranz-Itúrbide, Guillermo P Vicent, Florenci Serras, Isabel Fabregat, Montserrat Corominas.
      The mammalian liver exhibits remarkable regenerative capabilities after injury or resection. Central to this process is the precise modulation of gene expression, driven by changes in chromatin structure and the temporal activation of distal regulatory elements. In this study, we integrated chromatin accessibility and transcriptomic data after partial hepatectomy in mice. We show that the expression of crucial regeneration genes is orchestrated by a diverse array of cis-regulatory elements, including regeneration-specific enhancers and enhancers repurposed from various developmental stages. These enhancers collaborate to activate the transcriptional programs required for hepatocyte priming and proliferation, with their activity initially regulated by the activator protein-1 (AP-1) complex and ATF3, and subsequently by nuclear factor erythroid 2 (NFE2)-related factor 2 (NRF2) during proliferation. Our results also indicate that hepatic regeneration involves the repression of enhancers regulating liver-specific metabolic functions, particularly those involved in lipid metabolism. This study provides a genome-wide atlas of enhancer-gene interactions, offering new insights into the regulatory mechanisms underlying liver regeneration.
    Keywords:  ATF3; NRF2; chromatin dynamics; development; enhancers; hepatocyte; liver; regeneration; transcription factors
    DOI:  https://doi.org/10.1016/j.xgen.2025.100887
  22. Nat Commun. 2025 May 23. 16(1): 4786
    Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity.
    Michael Kosicki, Dianne Laboy Cintrón, Pia Keukeleire, Max Schubach, Nicholas F Page, Ilias Georgakopoulos-Soares, Jennifer A Akiyama, Ingrid Plajzer-Frick, Catherine S Novak, Momoe Kato, Riana D Hunter, Kianna von Maydell, Sarah Barton, Patrick Godfrey, Erik Beckman, Stephan J Sanders, Martin Kircher, Len A Pennacchio, Nadav Ahituv.
      High-throughput massively parallel reporter assays (MPRAs) and phenotype-rich in vivo transgenic mouse assays are two potentially complementary ways to study the impact of noncoding variants associated with psychiatric diseases. Here, we investigate the utility of combining these assays. Specifically, we carry out an MPRA in induced human neurons on over 50,000 sequences derived from fetal neuronal ATAC-seq datasets and enhancers validated in mouse assays. We also test the impact of over 20,000 variants, including synthetic mutations and 167 common variants associated with psychiatric disorders. We find a strong and specific correlation between MPRA and mouse neuronal enhancer activity. Four out of five tested variants with significant MPRA effects affected neuronal enhancer activity in mouse embryos. Mouse assays also reveal pleiotropic variant effects that could not be observed in MPRA. Our work provides a catalog of functional neuronal enhancers and variant effects and highlights the effectiveness of combining MPRAs and mouse transgenic assays.
    DOI:  https://doi.org/10.1038/s41467-025-60064-1
  23. G3 (Bethesda). 2025 May 23. pii: jkaf089. [Epub ahead of print]
    A single high-zinc activation enhancer can control two genes oriented head-to-head in Caenorhabditis elegans.
    Hanwenheng Liu, Brian Earley, Adelita Mendoza, Patrick Hunt, Sean Teng, Daniel Luke Schneider, Kerry Kornfeld.
      Enhancers play critical roles in gene expression, but a full understanding of their complex functions has yet to be defined. The cellular response to excess zinc levels in Caenorhabditis elegans requires the HIZR-1 transcription factor, which binds the high-zinc activation (HZA) enhancer in the promoters of multiple target genes. Cadmium hijacks the excess zinc response by binding and activating HIZR-1. By analyzing the genome-wide transcriptional response to excess zinc and cadmium, we identified two positions in the genome where head-to-head oriented genes are both induced by metals. In both examples, a single predicted HZA enhancer is positioned between the two translational start sites. We hypothesized that a single enhancer can control both head-to-head genes, an arrangement that has not been extensively characterized. To test this hypothesis, we used CRISPR genome editing to precisely delete the HZAmT enhancer positioned between mtl-2 and T08G5.1; in this mutant, both head-to-head genes display severely reduced zinc-activated transcription, whereas zinc-activated transcription of more distant genes was not strongly affected. Deleting the HZAcF enhancer positioned between cdr-1 and F35E8.10 caused both head-to-head genes to display reduced cadmium-activated transcription, whereas cadmium-activated transcription of more distant genes was not strongly affected. These studies rigorously document that a single HZA enhancer can control two head-to-head genes, advancing our understanding of the diverse functions of enhancers.
    Keywords:   Caenorhabditis elegans ; HZA; WormBase; Zinc metabolism; divergent transcription; enhancer; high-zinc activation element
    DOI:  https://doi.org/10.1093/g3journal/jkaf089
  24. Nat Struct Mol Biol. 2025 May 16.
    DEK-nucleosome structure shows DEK modulates H3K27me3 and stem cell fate.
    Yunfan Shen, Yanhong Liu, Maochao Guo, Song Mao, Rui Chen, Mengran Wang, Zhengbo Li, Yue Li, Wan Chen, Fang Chen, Baixing Wu, Chongyuan Wang, Wei Chen, Huanhuan Cui, Kai Yuan, Hongda Huang.
      DEK is a highly conserved chromatin-associated oncoprotein that has important roles in regulating chromatin dynamics and stem cell fate. Dysregulation of DEK is associated with stem cell dysfunction and cancers, including acute myeloid leukemia. Despite its importance in chromatin regulation, the structural mechanisms underlying DEK's interaction with chromatin and its influence on gene regulation remain poorly understood. Here we combined cryogenic electron microscopy (cryo-EM), biochemical and cellular approaches to investigate the molecular mechanisms and functional importance of DEK's interaction with chromatin. Our cryo-EM structures reveal the structural basis of the DEK-nucleosome interaction. Biochemical and cellular results demonstrate that this interaction is crucial for DEK deposition onto chromatin. Furthermore, our results reveal that DEK safeguards mouse embryonic stem cells from acquiring primitive endoderm fates by modulating the repressive histone mark H3K27me3. Together, our study provides crucial molecular insights into the structure and function of DEK, establishing a framework for understanding its roles in chromatin biology and cell fate determination.
    DOI:  https://doi.org/10.1038/s41594-025-01559-9
  25. PLoS Comput Biol. 2025 May 23. 21(5): e1013114
    MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures.
    Yuxiang Zhan, Francesco Musella, Frank Alber.
      The genome is organized into distinct chromatin compartments with at least two main classes, a transcriptionally active A and an inactive B compartment, broadly corresponding to euchromatin and heterochromatin. Chromatin regions within the same compartment preferentially interact with each other over regions in the opposite compartment. A/B compartments are traditionally identified from ensemble Hi-C contact frequency matrices using principal component analysis of their covariance matrices. However, defining compartments at the single-cell level from sparse single-cell Hi-C data is challenging, especially since homologous copies are often not resolved. To address this, we present MaxComp, an unsupervised method, for inferring single-cell A/B compartments based on 3D geometric considerations in single-cell chromosome structures-derived either from multiplexed FISH-omics imaging or 3D structure models derived from Hi-C data. By representing each 3D chromosome structure as an undirected graph with edge-weights encoding structural information, MaxComp reformulates compartment prediction as a variant of the Max-cut problem, solved using semidefinite graph programming (SPD) to optimally partition the graph into two structural compartments. Our results show that the population average of MaxComp single-cell compartment annotations closely matches those derived from ensemble Hi-C principal component analysis, demonstrating that compartmentalization can be recovered from geometric principles alone, using only the 3D coordinates and nuclear microenvironment of chromatin regions. Our approach reveals widespread cell-to-cell variability in compartment organization, with substantial heterogeneity across genomic loci. When applied to multiplexed FISH imaging data, MaxComp also uncovers relationships between compartment annotations and transcriptional activity at the single-cell level. In summary, MaxComp offers a new framework for understanding chromatin compartmentalization in single cells, connecting 3D genome architecture, and transcriptional activity with the cell-to-cell variations of chromatin compartments.
    DOI:  https://doi.org/10.1371/journal.pcbi.1013114
  26. Nat Commun. 2025 May 23. 16(1): 4800
    The ALX4 dimer structure provides insight into how disease alleles impact function.
    Brittany Cain, Zhenyu Yuan, Evelyn Thoman, Rhett A Kovall, Brian Gebelein.
      How homeodomain proteins gain sufficient DNA binding specificity to regulate diverse processes is a long-standing question. Here, we determine how the ALX4 Paired-like protein achieves DNA binding specificity for a TAAT-NNN-ATTA dimer site. We first show that ALX4 binds this motif independently of its co-factor, TWIST1, in cranial neural crest cells. Structural analysis identifies seven ALX4 residues that participate in dimer binding, many of which are conserved across the Paired-like family, but not other homeodomain proteins. Unexpectedly, the two ALX4 proteins within the dimer use distinct residues to form asymmetric protein-protein and protein-DNA interactions and mediate cooperativity. Moreover, we find that ALX4 cooperativity is required for transcriptional activation and that ALX4 disease variants cause distinct molecular defects that include loss of cooperativity. These findings provide insights into how Paired-like factors gain DNA specificity and show how disease variants can be stratified based on their molecular defects.
    DOI:  https://doi.org/10.1038/s41467-025-59728-9
  27. Nat Commun. 2025 May 19. 16(1): 4658
    DNA replication timing reveals genome-wide features of transcription and fragility.
    Francisco Berkemeier, Peter R Cook, Michael A Boemo.
      DNA replication in humans requires precise regulation to ensure accurate genome duplication and maintain genome integrity. A key indicator of this regulation is replication timing, which reflects the interplay between origin firing and fork dynamics. We present a high-resolution (1-kilobase) mathematical model that infers firing rate distributions from Repli-seq timing data across multiple cell lines, enabling a genome-wide comparison between predicted and observed replication. Notably, regions where the model and data diverge often overlap fragile sites and long genes, highlighting the influence of genomic architecture on replication dynamics. Conversely, regions of strong concordance are associated with open chromatin and active promoters, where elevated firing rates facilitate timely fork progression and reduce replication stress. In this work, we provide a valuable framework for exploring the structural interplay between replication timing, transcription, and chromatin organisation, offering insights into the mechanisms underlying replication stress and its implications for genome stability and disease.
    DOI:  https://doi.org/10.1038/s41467-025-59991-w
  28. Cell Genom. 2025 May 13. pii: S2666-979X(25)00134-X. [Epub ahead of print] 100878
    Integrative characterization of MYC RNA-binding function.
    Sihan Li, Zehua Wang, Xiaofei Wang, Yifei Wang, Dhamotharan Pattarayan, Yu Zhang, Phuong Nguyen, Avishek Bhuniya, Yuang Chen, Haozhe Huang, Yixian Huang, Luxuan Wang, Junmei Wang, Song Li, Min Zhang, Yang Liu, Nara Lee, Da Yang.
      Emerging evidence suggests that MYC interacts with RNAs. Here, we performed an integrative characterization of MYC as an RNA-binding protein in six cell lines. We found that MYC binds to a myriad of RNAs with high affinity for guanosine-rich RNAs. Global and specific depletion of RNAs reduces MYC chromatin occupancy. Mechanistically, two highly conserved sequences, amino acids 355-357 KRR and 364-367 RQRR, within the basic region of MYC are necessary for its RNA binding. Notably, alanine substitution of KRR abolishes MYC's RNA-binding ability both in vitro and in vivo, without affecting its ability to bind E-box DNA as part of the MYC:MAX dimer in vitro. The loss of RNA-binding function decreases MYC chromatin binding in vivo and attenuates its ability to promote gene expression, cell-cycle progression, and proliferation. Our study lays a foundation for future investigation into the role of RNAs in MYC-mediated transcriptional activation and oncogenic functions.
    Keywords:  CRISPR-Display; MYC; RNA-binding protein (RBP); TF RNA binding; arginine-rich motif; eCLIP; enhancer RNA; gene regulation; guanosine-rich RNA; rChIP
    DOI:  https://doi.org/10.1016/j.xgen.2025.100878
  29. Genome Biol. 2025 May 19. 26(1): 129
    RobusTAD: reference panel based annotation of nested topologically associating domains.
    Yanlin Zhang, Rola Dali, Mathieu Blanchette.
      Topologically associating domains (TADs) are fundamental units of 3D genomes and play essential roles in gene regulation. Hi-C data suggests a hierarchical organization of TADs. Accurately annotating nested TADs from Hi-C data remains challenging, both in terms of the precise identification of boundaries and the correct inference of hierarchies. While domain boundary is relatively well conserved across cells, few approaches have taken advantage of this fact. Here, we present RobusTAD to annotate TAD hierarchies. It incorporates additional Hi-C data to refine boundaries annotated from the study sample. RobusTAD outperforms existing tools at boundary and domain annotation across several benchmarking tasks.
    Keywords:  Dynamic programming; Hi-C; Nonparametric test; TAD
    DOI:  https://doi.org/10.1186/s13059-025-03568-9
  30. Nat Commun. 2025 May 17. 16(1): 4607
    CREATE: cell-type-specific cis-regulatory element identification via discrete embedding.
    Xuejian Cui, Qijin Yin, Zijing Gao, Zhen Li, Xiaoyang Chen, Hairong Lv, Shengquan Chen, Qiao Liu, Wanwen Zeng, Rui Jiang.
      Cis-regulatory elements (CREs), including enhancers, silencers, promoters and insulators, play pivotal roles in orchestrating gene regulatory mechanisms that drive complex biological traits. However, current approaches for CRE identification are predominantly sequence-based and typically focus on individual CRE types, limiting insights into their cell-type-specific functions and regulatory dynamics. Here, we present CREATE, a multimodal deep learning framework based on Vector Quantized Variational AutoEncoder, tailored for comprehensive CRE identification and characterization. CREATE integrates genomic sequences, chromatin accessibility, and chromatin interaction data to generate discrete CRE embeddings, enabling accurate multi-class classification and robust characterization of CREs. CREATE excels in identifying cell-type-specific CREs, and provides quantitative and interpretable insights into CRE-specific features, uncovering the underlying regulatory codes. By facilitating large-scale prediction of CREs in specific cell types, CREATE enhances the recognition of disease- or phenotype-associated biological variabilities of CREs, thus advancing our understanding of gene regulatory landscapes and their roles in health and disease.
    DOI:  https://doi.org/10.1038/s41467-025-59780-5
  31. Genome Res. 2025 May 20. pii: gr.280051.124. [Epub ahead of print]
    Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise.
    Aliza Batya Rubenstein, Gregory R Smith, Zidong Zhang, Xi Chen, Toby Leigh Chambers, Frederique Ruf-Zamojski, Natalia Mendelev, Wan Sze Cheng, Michel Zamojski, Mary Anne S Amper, Venugopalan D Nair, Andrew Reid Marderstein, Stephen B Montgomery, Olga G Troyanskaya, Elena Zaslavsky, Todd Trappe, Scott Trappe, Stuart C Sealfon.
      Endurance exercise induces multi-system adaptations that improve performance and benefit health. Gene regulatory circuit responses within individual skeletal muscle cell types, which are key mediators of exercise effects, have not been studied. We mapped transcriptome, chromatin, and regulatory circuit responses to acute endurance exercise in muscle using same-cell RNA-seq/ATAC-seq multiome assay. High-quality data was obtained from 37,154 nuclei comprising 14 cell types in vastus lateralis samples collected before and 3.5 hours after either 40 min cycling exercise at 70% VO2max or 40 min supine rest. Both shared and cell type specific regulatory programs were identified. Differential gene expression and accessibility sites were largely distinct within nuclei for each cell type and muscle fiber, with the largest numbers of regulatory events observed in the three muscle fiber types (slow, fast, and intermediate) and lumican (LUM) expressing fibro-adipogenic progenitor cells. Single-cell regulatory circuit triad reconstruction (transcription factor, chromatin interaction site, regulated gene) also identified largely distinct gene regulatory circuits modulated by exercise in the three muscle fiber types and LUM-expressing fibro-adipogenic progenitor cells, involving a total of 328 transcription factors acting at chromatin sites regulating 2,025 genes. This web-accessible single-cell dataset and regulatory circuitry map serve as a resource for understanding the molecular underpinnings of the metabolic and physiological effects of exercise and to guide interpretation of the exercise response literature in bulk tissue.
    DOI:  https://doi.org/10.1101/gr.280051.124
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