bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2025–03–02
33 papers selected by
Connor Rogerson, University of Cambridge
  1. Genome-coverage single-cell histone modifications for embryo lineage tracing.
  2. Long-range enhancer-controlled genes are hypersensitive to regulatory factor perturbations.
  3. Construction of an Atlas of transcription factor binding during mouse development identifies popular regulatory regions.
  4. Cell type-specific 3D-genome organization and transcription regulation in the brain.
  5. A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin.
  6. Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility.
  7. Multiomic QTL mapping reveals phenotypic complexity of GWAS loci and prioritizes putative causal variants.
  8. Epigenetic control of cell identities from epiblast to gastrulation.
  9. Inhibition of PRC2 enables self-renewal of blastoid-competent naive pluripotent stem cells from chimpanzee.
  10. Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in early mouse embryos.
  11. Deep learning imputes DNA methylation states in single cells and enhances the detection of epigenetic alterations in schizophrenia.
  12. Extensive mutual influences of SMC complexes shape 3D genome folding.
  13. The AaFoxA factor regulates female reproduction through chromatin remodeling in the mosquito vector Aedes aegypti.
  14. Macromolecular and cytological changes in fission yeast G0 nuclei.
  15. ETV4 and ETV5 orchestrate FGF-mediated lineage specification and epiblast maturation during early mouse development.
  16. Hypoxia-induced ATF3 escalates breast cancer invasion by increasing collagen deposition via P4HA1.
  17. DECA: harnessing interpretable transformer model for cellular deconvolution of chromatin accessibility profile.
  18. The lncRNA DUBR is regulated by CTCF and coordinates chromatin landscape and gene expression in hematopoietic cells.
  19. Decoding heterogeneous single-cell perturbation responses.
  20. CTCF regulates global chromatin accessibility and transcription during rod photoreceptor development.
  21. p85β acts as a transcription cofactor and cooperates with BCLAF1 in the nucleus.
  22. Pcf11/Spt5 condensates stall RNA polymerase II to facilitate termination and piRNA-guided heterochromatin formation.
  23. Linking DNA-packing density distribution and TAD boundary locations.
  24. The transcription factor SRF regulates MERVL retrotransposons and gene expression during zygotic genome activation.
  25. ETVs dictate hPSC differentiation by tuning biophysical properties.
  26. Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development.
  27. Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2.
  28. Control of ciliary transcriptional programs during spermatogenesis by antagonistic transcription factors.
  29. Pluripotency factor Tex10 finetunes Wnt signaling for spermatogenesis and primordial germ cell development.
  30. Rescuing DNMT1 fails to fully reverse the molecular and functional repercussions of its loss in mouse embryonic stem cells.
  31. Glycolytic reprogramming shapes the histone acetylation profile of activated CD4+ T cells in juvenile idiopathic arthritis.
  32. Maternal PRDM10 activates essential genes for oocyte-to-embryo transition.
  33. A Distinct Mechanism of RNA Recognition by the Transcription Factor GATA1.
  1. Nature. 2025 Feb 26.
    Genome-coverage single-cell histone modifications for embryo lineage tracing.
    Min Liu, Yanzhu Yue, Xubin Chen, Kexin Xian, Chao Dong, Ming Shi, Haiqing Xiong, Kang Tian, Yuzhe Li, Qiangfeng Cliff Zhang, Aibin He.
      Substantial epigenetic resetting during early embryo development from fertilization to blastocyst formation ensures zygotic genome activation and leads to progressive cellular heterogeneities1-3. Mapping single-cell epigenomic profiles of core histone modifications that cover each individual cell is a fundamental goal in developmental biology. Here we develop target chromatin indexing and tagmentation (TACIT), a method that enabled genome-coverage single-cell profiling of seven histone modifications across mouse early embryos. We integrated these single-cell histone modifications with single-cell RNA sequencing data to chart a single-cell resolution epigenetic landscape. Multimodal chromatin-state annotations showed that the onset of zygotic genome activation at the early two-cell stage already primes heterogeneities in totipotency. We used machine learning to identify totipotency gene regulatory networks, including stage-specific transposable elements and putative transcription factors. CRISPR activation of a combination of these identified transcription factors induced totipotency activation in mouse embryonic stem cells. Together with single-cell co-profiles of multiple histone modifications, we developed a model that predicts the earliest cell branching towards the inner cell mass and the trophectoderm in latent multimodal space and identifies regulatory elements and previously unknown lineage-specifying transcription factors. Our work provides insights into single-cell epigenetic reprogramming, multimodal regulation of cellular lineages and cell-fate priming during mouse pre-implantation development.
    DOI:  https://doi.org/10.1038/s41586-025-08656-1
  2. Cell Genom. 2025 Feb 20. pii: S2666-979X(25)00034-5. [Epub ahead of print] 100778
    Long-range enhancer-controlled genes are hypersensitive to regulatory factor perturbations.
    Sjoerd J D Tjalsma, Niels J Rinzema, Marjon J A M Verstegen, Michelle J Robers, Andrea Nieto-Aliseda, Richard A Gremmen, Amin Allahyar, Mauro J Muraro, Peter H L Krijger, Wouter de Laat.
      Cell-type-specific gene activation is regulated by enhancers, sometimes located at large genomic distances from target gene promoters. Whether distal enhancers require specific factors to orchestrate gene regulation remains unclear. Here, we used enhancer distance-controlled reporter screens to find candidate factors. We depleted them and employed activity-by-contact predictions to genome-wide classify genes based on enhancer distance. Predicted distal enhancers typically control tissue-restricted genes and often are strong enhancers. We find cohesin, but also mediator, most specifically required for long-range activation, with cohesin repressing short-range gene activation and prioritizing distal over proximal HBB genes competing for shared enhancers. Long-range controlled genes are also most sensitive to perturbations of other regulatory proteins and to BET inhibitor JQ1, this being more a consequence of their distinct enhancer features than distance. Our work predicts that lengthening of intervening sequences can help limit the expression of target genes to specialized cells with optimal trans-factor environments.
    Keywords:  3D genome; cancer; chromatin; cohesin; development; enhancers; mediator; transcription
    DOI:  https://doi.org/10.1016/j.xgen.2025.100778
  3. Development. 2025 Feb 27. pii: dev.204311. [Epub ahead of print]
    Construction of an Atlas of transcription factor binding during mouse development identifies popular regulatory regions.
    Anna Nordin, Gianluca Zambanini, Mattias Jonasson, Tamina Weiss, Yorick van de Grift, Pierfrancesco Pagella, Claudio Cantù.
      Gene regulators physically associate to the genome, in a combinatorial fashion, to drive tissue-specific gene expression. Uncovering the genome-wide activity of all gene regulators across tissues is therefore needed to understand gene regulation during development. Here, we take a first step towards this goal. Using CUT&RUN, we systematically mapped genome-wide binding profiles of key transcription factors and cofactors that mediate ontogenetically relevant signaling pathways in select mouse tissues at two developmental stages. Computation of the datasets unveiled tissue and time-specific activity for each gene regulator. We identified "popular" regulatory regions that are bound by a multitude of regulators, which tend to be more evolutionarily conserved. Consistently, they lie near the TSS of genes whose dysregulation causes early embryonic lethality. Moreover, the human homologs of these regions are similarly bound by many gene regulators and are highly conserved, indicating a retained relevance for human development. This work constitutes a decisive step towards understanding how the genome is simultaneously read and used by gene regulators in a holistic fashion to drive embryonic development.
    Keywords:  CUT&RUN; Chromatin; Development; Gene regulation; Transcription factors
    DOI:  https://doi.org/10.1242/dev.204311
  4. Sci Adv. 2025 Feb 28. 11(9): eadv2067
    Cell type-specific 3D-genome organization and transcription regulation in the brain.
    Shiwei Liu, Cosmos Yuqi Wang, Pu Zheng, Bojing Blair Jia, Nathan R Zemke, Peter Ren, Hannah L Park, Bing Ren, Xiaowei Zhuang.
      3D organization of the genome plays a critical role in regulating gene expression. How 3D-genome organization differs among different cell types and relates to cell type-dependent transcriptional regulation remains unclear. Here, we used genome-scale DNA and RNA imaging to investigate 3D-genome organization in transcriptionally distinct cell types in the mouse cerebral cortex. We uncovered a wide spectrum of differences in the nuclear architecture and 3D-genome organization among different cell types, ranging from the size of the cell nucleus to higher-order chromosome structures and radial positioning of chromatin loci within the nucleus. These cell type-dependent variations in nuclear architecture and chromatin organization exhibit strong correlations with both the total transcriptional activity of the cell and transcriptional regulation of cell type-specific marker genes. Moreover, we found that the methylated DNA binding protein MeCP2 promotes active-inactive chromatin segregation and regulates transcription in a nuclear radial position-dependent manner that is highly correlated with its function in modulating active-inactive chromatin compartmentalization.
    DOI:  https://doi.org/10.1126/sciadv.adv2067
  5. Mol Cell. 2025 Feb 19. pii: S1097-2765(25)00099-1. [Epub ahead of print]
    A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin.
    Merle Skribbe, Charlotte Soneson, Michael B Stadler, Michaela Schwaiger, Vishnu N Suma Sreechakram, Vytautas Iesmantavicius, Daniel Hess, Eliza Pandini Figueiredo Moreno, Sigurd Braun, Jan Seebacher, Sebastien A Smallwood, Marc Bühler.
      Transcription factors (TFs) are key regulators of gene expression, yet many of their targets and modes of action remain unknown. In Schizosaccharomyces pombe, one-third of TFs are solely homology predicted, with few experimentally validated. We created a comprehensive library of 89 endogenously tagged S. pombe TFs, mapping their protein and chromatin interactions using immunoprecipitation-mass spectrometry and chromatin immunoprecipitation sequencing. Our study identified protein interactors for half the TFs, with over a quarter potentially forming stable complexes. We discovered DNA-binding sites for most TFs across 2,027 unique genomic regions, revealing motifs for 38 TFs and uncovering a complex network of extensive TF cross- and autoregulation. Characterization of the largest TF family revealed conserved DNA sequence preferences but diverse binding patterns and identified a repressive heterodimer, Ntu1/Ntu2, linked to perinuclear gene localization. Our TFexplorer webtool makes all data interactively accessible, offering insights into TF interactions and regulatory mechanisms with broad biological relevance.
    Keywords:  ChIP-sequencing; Nattou complex; TF binding motifs; TFexplorer; binuclear zinc cluster TFs; fission yeast library; high occupancy target (HOT) regions; immunoprecipitation-mass spectrometry; transcription factor interactions
    DOI:  https://doi.org/10.1016/j.molcel.2025.01.032
  6. Nucleic Acids Res. 2025 Feb 08. pii: gkaf101. [Epub ahead of print]53(4):
    Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility.
    Peter Chovanec, Yi Yin.
      Single-cell combinatorial indexing (sci) methods have addressed major limitations of throughput and cost for many single-cell modalities. With the incorporation of linear amplification and three-level barcoding in our suite of methods called sci-L3, we further addressed the limitations of uniformity in single-cell genome amplification. Here, we build on the generalizability of sci-L3 by extending it to template strand sequencing (sci-L3-Strand-seq), genome conformation capture (sci-L3-Hi-C), and the joint profiling of RNA and chromatin accessibility (sci-L3-RNA/ATAC). We demonstrate the ease of adapting sci-L3 to these new modalities by only requiring a single-step modification of the original protocol. As a proof of principle, we show our ability to detect sister chromatid exchanges, genome compartmentalization, and cell state-specific features in thousands of single cells. We anticipate sci-L3 to be compatible with additional modalities, including DNA methylation (sci-MET) and chromatin-associated factors (CUT&Tag), and ultimately enable a multi-omics readout of them.
    DOI:  https://doi.org/10.1093/nar/gkaf101
  7. Cell Genom. 2025 Feb 16. pii: S2666-979X(25)00031-X. [Epub ahead of print] 100775
    Multiomic QTL mapping reveals phenotypic complexity of GWAS loci and prioritizes putative causal variants.
    iPSCORE Consortium
      Most GWAS loci are presumed to affect gene regulation; however, only ∼43% colocalize with expression quantitative trait loci (eQTLs). To address this colocalization gap, we map eQTLs, chromatin accessibility QTLs (caQTLs), and histone acetylation QTLs (haQTLs) using molecular samples from three early developmental-like tissues. Through colocalization, we annotate 10.4% (n = 540) of GWAS loci in 15 traits by QTL phenotype, temporal specificity, and complexity. We show that integration of chromatin QTLs results in a 2.3-fold higher annotation rate of GWAS loci because they capture distal GWAS loci missed by eQTLs, and that 5.4% (n = 13) of GWAS colocalizing eQTLs are early developmental specific. Finally, we utilize the iPSCORE multiomic QTLs to prioritize putative causal variants overlapping transcription factor motifs to elucidate the potential genetic underpinnings of 296 GWAS-QTL colocalizations.
    Keywords:  GWAS; QTLs; chromatin accessibility QTLs; expression QTLs; histone acetylation QTLs; iPSC-derived cardiovascular progenitors; iPSC-derived pancreatic precursors; induced pluripotent stem cells; multiomic QTLs; quantitative trait loci
    DOI:  https://doi.org/10.1016/j.xgen.2025.100775
  8. FEBS J. 2025 Feb 22.
    Epigenetic control of cell identities from epiblast to gastrulation.
    Katrin M Schüle, Simone Probst.
      Epigenetic modifications of chromatin are essential for the establishment of cell identities during embryogenesis. Between embryonic days 3.5-7.5 of murine development, major cell lineage decisions are made that discriminate extraembryonic and embryonic tissues, and the embryonic primary germ layers are formed, thereby laying down the basic body plan. In this review, we cover the contribution of dynamic chromatin modifications by DNA methylation, changes of chromatin accessibility, and histone modifications, that in combination with transcription factors control gene expression programs of different cell types. We highlight the differences in regulation of enhancer and promoter marks and discuss their requirement in cell lineage specification. Importantly, in many cases, lineage-specific targeting of epigenetic modifiers is carried out by pioneer or master transcription factors, that in sum mediate the chromatin landscape and thereby control the transcription of cell-type-specific gene programs and thus, cell identities.
    Keywords:  DNA methylation; embryonic stem cells; epigenetics; gastrulation; germ layers; histone modifications; mouse embryo; nucleosome remodeling; transcription factors
    DOI:  https://doi.org/10.1111/febs.70024
  9. Cell Stem Cell. 2025 Feb 21. pii: S1934-5909(25)00041-4. [Epub ahead of print]
    Inhibition of PRC2 enables self-renewal of blastoid-competent naive pluripotent stem cells from chimpanzee.
    Tao Huang, Arthur Radley, Ayaka Yanagida, Zhili Ren, Francesca Carlisle, Somayyeh Tahajjodi, Dongwan Kim, Paul O'Neill, James Clarke, Madeline A Lancaster, Zoe Heckhausen, Jingran Zhuo, João Pedro Agostinho de Sousa, Petra Hajkova, Ferdinand von Meyenn, Hiroo Imai, Hiromitsu Nakauchi, Ge Guo, Austin Smith, Hideki Masaki.
      Naive pluripotent stem cells (PSCs) are counterparts of early epiblast in the mammalian embryo. Mouse and human naive PSCs differ in self-renewal requirements and extraembryonic lineage potency. Here, we investigated the generation of chimpanzee naive PSCs. Colonies generated by resetting or reprogramming failed to propagate. We discovered that self-renewal is enabled by inhibition of Polycomb repressive complex 2 (PRC2). Expanded cells show global transcriptome proximity to human naive PSCs and embryo pre-implantation epiblast, with shared expression of a subset of pluripotency transcription factors. Chimpanzee naive PSCs can transition to multilineage competence or can differentiate into trophectoderm and hypoblast, forming tri-lineage blastoids. They thus provide a higher primate comparative model for studying pluripotency and early embryogenesis. Genetic deletions confirm that PRC2 mediates growth arrest. Further, inhibition of PRC2 overcomes a roadblock to feeder-free propagation of human naive PSCs. Therefore, excess deposition of chromatin modification H3K27me3 is an unexpected barrier to naive PSC self-renewal.
    Keywords:  Polycomb; developmental drift; epiblast; higher primate; mammalian early embryo; naive pluripotency; pluripotent stem cells; self-renewal; single-cell transcriptomics; stem cell-based embryo model
    DOI:  https://doi.org/10.1016/j.stem.2025.02.002
  10. Elife. 2025 Feb 27. pii: RP100735. [Epub ahead of print]13
    Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in early mouse embryos.
    Yanlin Hou, Zhengwen Nie, Qi Jiang, Sergiy Velychko, Sandra Heising, Ivan Bedzhov, Guangming Wu, Kenjiro Adachi, Hans R Scholer.
      During the first lineage segregation, mammalian embryos generate the inner cell mass (ICM) and trophectoderm (TE). ICM gives rise to the epiblast (EPI) that forms all cell types of the body, an ability referred to as pluripotency. The molecular mechanisms that induce pluripotency in embryos remain incompletely elucidated. Using knockout (KO) mouse models in conjunction with low-input ATAC-seq and RNA-seq, we found that Oct4 and Sox2 gradually come into play in the early ICM, coinciding with the initiation of Sox2 expression. Oct4 and Sox2 activate the pluripotency-related genes through the putative OCT-SOX enhancers in the early ICM. Furthermore, we observed a substantial reorganization of chromatin landscape and transcriptome from the morula to the early ICM stages, which was partially driven by Oct4 and Sox2, highlighting their pivotal role in promoting the developmental trajectory toward the ICM. Our study provides new insights into the establishment of the pluripotency network in mouse preimplantation embryos.
    Keywords:  Oct4; Sox2; chromatin accessibility; developmental biology; embryonic development; inner cell mass; mouse; transcriptome
    DOI:  https://doi.org/10.7554/eLife.100735
  11. Cell Genom. 2025 Feb 15. pii: S2666-979X(25)00030-8. [Epub ahead of print] 100774
    Deep learning imputes DNA methylation states in single cells and enhances the detection of epigenetic alterations in schizophrenia.
    Jiyun Zhou, Chongyuan Luo, Hanqing Liu, Matthew G Heffel, Richard E Straub, Joel E Kleinman, Thomas M Hyde, Joseph R Ecker, Daniel R Weinberger, Shizhong Han.
      DNA methylation (DNAm) is a key epigenetic mark with essential roles in gene regulation, mammalian development, and human diseases. Single-cell technologies enable profiling DNAm at cytosines in individual cells, but they often suffer from low coverage for CpG sites. We introduce scMeFormer, a transformer-based deep learning model for imputing DNAm states at each CpG site in single cells. Comprehensive evaluations across five single-nucleus DNAm datasets from human and mouse demonstrate scMeFormer's superior performance over alternative models, achieving high-fidelity imputation even with coverage reduced to 10% of original CpG sites. Applying scMeFormer to a single-nucleus DNAm dataset from the prefrontal cortex of patients with schizophrenia and controls identified thousands of schizophrenia-associated differentially methylated regions that would have remained undetectable without imputation and added granularity to our understanding of epigenetic alterations in schizophrenia. We anticipate that scMeFormer will be a valuable tool for advancing single-cell DNAm studies.
    Keywords:  DNA methylation; deep learning; imputation; schizophrenia; transformer
    DOI:  https://doi.org/10.1016/j.xgen.2025.100774
  12. Nature. 2025 Feb 26.
    Extensive mutual influences of SMC complexes shape 3D genome folding.
    Han Zhao, Lirong Shu, Shiyi Qin, Fangxuan Lyu, Fuhai Liu, En Lin, Sijian Xia, Baiyue Wang, Manzhu Wang, Fengnian Shan, Yinzhi Lin, Lin Zhang, Yufei Gu, Gerd A Blobel, Kai Huang, Haoyue Zhang.
      Mammalian genomes are folded through the distinct actions of structural maintenance of chromosome (SMC) complexes, which include the chromatin loop-extruding cohesin (extrusive cohesin), the sister chromatid cohesive cohesin and the mitotic chromosome-associated condensins1-3. Although these complexes function at different stages of the cell cycle, they exist together on chromatin during the G2-to-M phase transition, when the genome structure undergoes substantial reorganization1,2. Yet, how the different SMC complexes affect each other and how their interactions orchestrate the dynamic folding of the three-dimensional genome remain unclear. Here we engineered all possible cohesin and condensin configurations on mitotic chromosomes to delineate the concerted, mutually influential action of SMC complexes. We show that condensin disrupts the binding of extrusive cohesin at CCCTC-binding factor (CTCF) sites, thereby promoting the disassembly of interphase topologically associating domains (TADs) and loops during mitotic progression. Conversely, extrusive cohesin impedes condensin-mediated mitotic chromosome spiralization. Condensin reduces peaks of cohesive cohesin, whereas cohesive cohesin antagonizes condensin-mediated longitudinal shortening of mitotic chromosomes. The presence of both extrusive and cohesive cohesin synergizes these effects and inhibits mitotic chromosome condensation. Extrusive cohesin positions cohesive cohesin at CTCF-binding sites. However, cohesive cohesin by itself cannot be arrested by CTCF molecules and is insufficient to establish TADs or loops. Moreover, it lacks loop-extrusion capacity, which indicates that cohesive cohesin has nonoverlapping functions with extrusive cohesin. Finally, cohesive cohesin restricts chromatin loop expansion mediated by extrusive cohesin. Collectively, our data describe a three-way interaction among major SMC complexes that dynamically modulates chromatin architecture during cell cycle progression.
    DOI:  https://doi.org/10.1038/s41586-025-08638-3
  13. Proc Natl Acad Sci U S A. 2025 Mar 04. 122(9): e2411758122
    The AaFoxA factor regulates female reproduction through chromatin remodeling in the mosquito vector Aedes aegypti.
    Yang Cheng, Xuesong Wang, Yike Ding, Houhong Zhang, Zhenyu Jia, Alexander S Raikhel.
      Female mosquitoes are vectors of many devastating human diseases because they require blood feeding to initiate reproduction. Thus, elucidation of molecular mechanisms managing female mosquito reproduction is essential. Although the regulation of gene expression during the mosquito gonadotrophic cycle has been studied in detail, how this process is controlled at the chromatin level remains unclear. Chromatin must be accessible for transcription factors (TFs) governing gene expression. A specialized class of TFs, called pioneer factors (PFs), binds and remodels closed chromatin, permitting other TFs to bind DNA and activate the gene expression. Here, we identified a homolog of the vertebrate PF FoxA in the mosquito Aedes aegypti and used the CRISPR-Cas9 system to generate mosquitoes deficient in AaFoxA. We found that ovary development was severely retarded in mutant females. Multiomics and molecular biology analyses have shown that AaFoxA increased histone acetylation and decreased methylation of H3K27 by controlling the chromatin accessibility of histone modification enzymes and chromatin remodelers. AaFoxA is bound to the loci of chromatin remodelers, changing their chromatin accessibility and modulating their temporal expression patterns. AaFoxA increased the accessibility of the ecdysone receptor (EcR) and E74 loci, indicating the important role of AaFoxA in the hormonal regulation of mosquito reproductive events. Further, the CUT&RUN and ATAC-seq analyses revealed that AaFoxA temporarily bound closed chromatin, making it differentially accessible during the mosquito gonadotrophic cycle. Hence, this study demonstrates that AaFoxA modulates chromatin dynamics throughout female mosquito reproduction.
    Keywords:  CRISPR-Cas9; chromatin remodeling; histone modification; pioneer factor; transcription
    DOI:  https://doi.org/10.1073/pnas.2411758122
  14. J Cell Sci. 2025 Feb 27. pii: jcs.263654. [Epub ahead of print]
    Macromolecular and cytological changes in fission yeast G0 nuclei.
    Zhi Yang Tan, Shujun Cai, Saayli A Paithankar, Tingsheng Liu, Xin Nie, Jian Shi, Lu Gan.
      When starved of nitrogen, fission yeast Schizosaccharomyces pombe cells enter a quiescent "G0" state with smaller nuclei and transcriptional repression. The genomics of S. pombe G0 cells has been well studied, but much of its nuclear cell biology remains unknown. Here we use confocal microscopy, immunoblots, and electron cryotomography to investigate the cytological, biochemical, and ultrastructural differences between S. pombe proliferating, G1-arrested, and G0 cell nuclei, with an emphasis on the histone acetylation, RNA polymerase II fates, and macromolecular complex packing. Compared to proliferating cells, G0 cells have lower levels of histone acetylation, nuclear RNA polymerase II, and active transcription. The G0 nucleus has similar macromolecular crowding yet fewer chromatin-associated multi-megadalton globular complexes. Induced histone hyperacetylation during nitrogen starvation results in cells that have larger nuclei and therefore less compact chromatin. However, these histone-hyperacetylated cells remain transcriptionally repressed with similar nuclear crowding. Canonical nucleosomes - those that resemble the crystal structure - are rare in proliferating, G1-arrested, and G0 cells. Our study therefore shows that extreme changes in nucleus physiology are possible without extreme reorganisation at the macromolecular level.
    Keywords:  Chromatin; Cryo-ET; Nucleus; Quiescence; Transcription; Yeast
    DOI:  https://doi.org/10.1242/jcs.263654
  15. Development. 2025 Feb 26. pii: dev.204278. [Epub ahead of print]
    ETV4 and ETV5 orchestrate FGF-mediated lineage specification and epiblast maturation during early mouse development.
    Claire S Simon, Woonyung Hur, Vidur Garg, Ying-Yi Kuo, Kathy K Niakan, Anna-Katerina Hadjantonakis.
      Cell fate decisions in early mammalian embryos are tightly regulated processes crucial for proper development. While FGF signaling plays key roles in early embryo patterning, its downstream effectors remain poorly understood. Our study demonstrates that the transcription factors Etv4 and Etv5 are critical mediators of FGF signaling in cell lineage specification and maturation in mouse embryos. We show that loss of Etv5 compromises primitive endoderm formation at pre-implantation stages. Furthermore, Etv4/5 deficiency delays naïve pluripotency exit and epiblast maturation, leading to elevated NANOG and reduced OTX2 expression within the blastocyst epiblast. As a consequence of delayed pluripotency progression, Etv4/5 deficient embryos exhibit anterior visceral endoderm migration defects post-implantation, a process essential for coordinated embryonic patterning and gastrulation initiation. Our results demonstrate the successive roles of these FGF signaling effectors in early lineage specification and embryonic body plan establishment, providing new insights into the molecular control of mammalian development.
    Keywords:  ETV; Epiblast; FGF; Pluripotency; Primitive endoderm
    DOI:  https://doi.org/10.1242/dev.204278
  16. Cell Death Dis. 2025 Feb 27. 16(1): 142
    Hypoxia-induced ATF3 escalates breast cancer invasion by increasing collagen deposition via P4HA1.
    Shruti Ganesh Dhamdhere, Anamika Bansal, Pranjal Singh, Parik Kakani, Shruti Agrawal, Atul Samaiya, Sanjeev Shukla.
      Activating transcription factors (ATFs), members of the adaptive-response gene family, participate in cellular processes to aid adaptations in response to extra and/or intracellular changes. In this study, we observed that one of the ATFs, Activating transcription factor 3 (ATF3), is upregulated under hypoxia via alterations in the epigenetic landscape of its promoter, followed by transcriptional upregulation. Under hypoxic conditions, Hypoxia-inducible factor 1-alpha (HIF1ɑ) alleviates methylation at the ATF3 promoter by recruiting TET1 and induces ATF3 transcription. In addition, our RNA-seq analysis showed that ATF3 globally affects transcription under hypoxia and controls the processes of EMT and cancer invasion by stimulating the transcription of Prolyl 4-Hydroxylase Subunit Alpha 1 (P4HA1), an enzyme which enhances invasion-conducive extracellular matrix (ECM) under hypoxic conditions. Prolyl hydroxylases play a critical role in the hydroxylation and deposition of collagen in the extracellular matrix (ECM) during the evolution of cancer, which is necessary for metastasis. Importantly, P4HA1 undergoes alternative splicing under hypoxia, where the inclusion of exon 9a is increased. Interestingly, involvement of ATF3 in P4HA1 splicing was also evident, as binding of ATF3 at intron 9a led to demethylation of this DNA region via recruitment of TET1. Furthermore, we also show that the demethylated DNA region of intron 9a then becomes accessible to CCCTC-binding factor (CTCF). Thus, a cascade of demethylation via ATF3 recruited TET1, followed by increased RNA Pol II pause at intron 9a via CTCF, leads to inclusion of exon 9a. The P4HA1 9a isoform leads to enhanced invasion under hypoxic conditions by increasing deposition of collagen in the ECM. These results reveal a novel hypoxia-induced HIF1ɑ-ATF3-P4HA1 axis which can potentially be exploited as a therapeutic target to impede EMT and ultimately breast cancer invasion. Hypoxia induced ATF3 regulates P4HA1 expression and alternative splicing to promote breast cancer invasion.
    DOI:  https://doi.org/10.1038/s41419-025-07461-y
  17. Brief Bioinform. 2024 Nov 22. pii: bbaf069. [Epub ahead of print]26(1):
    DECA: harnessing interpretable transformer model for cellular deconvolution of chromatin accessibility profile.
    Shijie Luo, Ming Zhu, Liquan Lin, Jiajing Xie, Shihao Lin, Ying Chen, Jiali Zhu, Jialiang Huang.
      The assay for transposase-accessible chromatin with sequencing (ATAC-seq) identifies chromatin accessibility across the genome, crucial for gene expression regulating. However, bulk ATAC-seq obscures cellular heterogeneity, while single-cell ATAC-seq suffers from issues such as sparsity and costliness. To this end, we introduce DECA, a sophisticated deep learning model based on vision transformer to deconvolve cell type information from bulk chromatin accessibility profiles, utilizing single-cell ATAC-seq datasets as reference for enhanced precision and resolution. Notably, patch attention generated by DECA's multi-head attention mechanism aligns with chromatin interactions detected by Hi-C. Additionally, DECA predicted lineage-specific cell composition changes due to genetic perturbation. The chromatin accessibility signatures predicted by DECA are enriched with cell-type specific genetic variations. Ultimately, we applied DECA on pan-cancer ATAC-seq datasets and demonstrated its capability to deconvolve cell type proportions with clinical significance. Taken together, DECA deconvolves cellular proportions and predicts their chromatin accessibility profiles from bulk chromatin accessibility data, which enable exploring the gene regulatory programs in development and diseases.
    Keywords:  ATAC-seq; cellular deconvolution; chromatin accessibility; single-cell; vision transformer
    DOI:  https://doi.org/10.1093/bib/bbaf069
  18. Nucleic Acids Res. 2025 Feb 08. pii: gkaf093. [Epub ahead of print]53(4):
    The lncRNA DUBR is regulated by CTCF and coordinates chromatin landscape and gene expression in hematopoietic cells.
    Hober Nelson Núñez-Martínez, Gustavo Tapia-Urzúa, Ángel Josué Cerecedo-Castillo, Carlos Alberto Peralta-Alvarez, Georgina Guerrero, Maite Huarte, Félix Recillas-Targa.
      Master hematopoietic transcription factors (TFs) and long noncoding RNAs (lncRNAs) coordinate shaping lineage-specific gene expression programs during hematopoietic differentiation. The architectural protein CCCTC-binding factor (CTCF) has emerged as a pivotal regulator of gene expression in cell differentiation. However, the relationship and its regulatory effect of CTCF on lncRNA genes in hematopoiesis remain elusive. We demonstrated that CTCF constrains the lncRNA DUBRtranscription throughout erythroid differentiation. DUBR is highly expressed in human hematopoietic stem and progenitor cells (HSPCs) but depleted in erythroblasts. DUBR perturbation dysregulates hematopoietic-erythroid cell differentiation genes and facilitates genome-wide activation of regulatory elements. A genomic map of RNA occupancy revealed that DUBR associates with a set of genes involved in regulating hematopoietic differentiation, including the erythroid repressor HES1, which targets a subset of regulatory elements of DUBR-dysregulated genes. Our results support the role of DUBR as a regulator of a hematopoietic differentiation gene program by coordinating the expression of genes and influencing their chromatin regulatory landscape.
    DOI:  https://doi.org/10.1093/nar/gkaf093
  19. Nat Cell Biol. 2025 Feb 26.
    Decoding heterogeneous single-cell perturbation responses.
    Bicna Song, Dingyu Liu, Weiwei Dai, Natalie F McMyn, Qingyang Wang, Dapeng Yang, Adam Krejci, Anatoly Vasilyev, Nicole Untermoser, Anke Loregger, Dongyuan Song, Breanna Williams, Bess Rosen, Xiaolong Cheng, Lumen Chao, Hanuman T Kale, Hao Zhang, Yarui Diao, Tilmann Bürckstümmer, Janet D Siliciano, Jingyi Jessica Li, Robert F Siliciano, Danwei Huangfu, Wei Li.
      Understanding how cells respond differently to perturbation is crucial in cell biology, but existing methods often fail to accurately quantify and interpret heterogeneous single-cell responses. Here we introduce the perturbation-response score (PS), a method to quantify diverse perturbation responses at a single-cell level. Applied to single-cell perturbation datasets such as Perturb-seq, PS outperforms existing methods in quantifying partial gene perturbations. PS further enables single-cell dosage analysis without needing to titrate perturbations, and identifies 'buffered' and 'sensitive' response patterns of essential genes, depending on whether their moderate perturbations lead to strong downstream effects. PS reveals differential cellular responses on perturbing key genes in contexts such as T cell stimulation, latent HIV-1 expression and pancreatic differentiation. Notably, we identified a previously unknown role for the coiled-coil domain containing 6 (CCDC6) in regulating liver and pancreatic cell fate decisions. PS provides a powerful method for dose-to-function analysis, offering deeper insights from single-cell perturbation data.
    DOI:  https://doi.org/10.1038/s41556-025-01626-9
  20. Proc Natl Acad Sci U S A. 2025 Mar 04. 122(9): e2416384122
    CTCF regulates global chromatin accessibility and transcription during rod photoreceptor development.
    Dahong Chen, Saumya Keremane, Silu Wang, Elissa P Lei.
      Chromatin architecture facilitates accurate transcription at a number of loci, but it remains unclear how much chromatin architecture is involved in global transcriptional regulation. Previous work has shown that rapid depletion of the architectural protein CTCF in cell culture alters global chromatin organization but results in surprisingly limited gene expression changes. This discrepancy has also been observed when other architectural proteins are depleted, and one possible explanation is that full transcriptional changes are masked by cellular heterogeneity. We tested this idea by performing multiomics analyses with sorted juvenile postmitotic mouse rods, which undergo synchronized development, and we identified CTCF-dependent regulation of global chromatin accessibility and gene expression. CTCF depletion leads to dysregulation of ~20% of the entire transcriptome (>3,000 genes) and ~41% of genome accessibility (>27,000 sites) before any prominent cellular or physiological phenotypes arise. Importantly, these changes are highly enriched for CTCF occupancy at euchromatin, suggesting direct CTCF binding and transcriptional regulation at these active loci. CTCF mainly promotes chromatin accessibility and frequently inhibits expression of these direct binding targets, which are enriched for binding motifs of transcription repressors. These findings provide different and sometimes opposite conclusions from previous studies, emphasizing the need to consider cellular heterogeneity and cell-type specificity when performing multiomics analyses. CTCF knockout rods undergo complete degeneration by adulthood, indicating an essential role for their viability. We conclude that the architectural protein CTCF binds chromatin and regulates global chromatin accessibility and transcription during rod development.
    Keywords:  CTCF; chromatin architecture; retinal development; rod; transcriptome
    DOI:  https://doi.org/10.1073/pnas.2416384122
  21. Nat Commun. 2025 Feb 27. 16(1): 2042
    p85β acts as a transcription cofactor and cooperates with BCLAF1 in the nucleus.
    Panpan Wang, Victor Cy Mak, Ling Rao, Qiuqiu Wu, Yuan Zhou, Rakesh Sharma, S Chul Kwon, Lydia Wt Cheung.
      p85β is a regulatory subunit of the phosphoinositide 3-kinase (PI3K). Emerging evidence suggests that p85β goes beyond its role in the PI3K and is functional in the nucleus. In this study, we discover that nuclear p85β is enriched at gene loci and regulates gene transcription and that this regulatory role contributes to the oncogenic potential of nuclear p85β. A multi-omics approach reveals the physical interaction and functional cooperativity between nuclear p85β and a transcription factor BCLAF1. We observe genome-wide co-occupancy of p85β and BCLAF1 at gene targets associated with transcriptional responses. Intriguingly, the targetome includes BCLAF1 of which transcription is activated by p85β and BCLAF1, indicating a positive autoregulation. While BCLAF1 recruits p85β to BCLAF1 loci, p85β facilitates the assembly of BCLAF1, the scaffold protein TRIM28 and the zinc finger transcription factor ZNF263, which together act in concert to activate BCLAF1 transcription. Collectively, this study provides functional evidence and mechanistic basis to support a role of nuclear p85β in modulating gene transcription.
    DOI:  https://doi.org/10.1038/s41467-025-56532-3
  22. Mol Cell. 2025 Feb 20. pii: S1097-2765(25)00057-7. [Epub ahead of print]
    Pcf11/Spt5 condensates stall RNA polymerase II to facilitate termination and piRNA-guided heterochromatin formation.
    Weiwei Liu, Lijun Deng, Ming Wang, Xiaojun Liu, Xuan Ouyang, Yuan Wang, Na Miao, Xiu Luo, Xueming Wu, Xiaohua Lu, Xiangjin Xv, Tianyu Zhang, Yu Li, Jinyao Ji, Zhenghao Qiao, Sheng Wang, Li Guan, Dong Li, Yunkun Dang, Chao Liu, Wei Li, Yadi Zhang, Zhenning Wang, Fei Xavier Chen, Chunlai Chen, Chengqi Lin, Wee Siong Sho Goh, Wenhao Zhou, Zhuojuan Luo, Pu Gao, Pilong Li, Yang Yu.
      The PIWI-interacting RNA (piRNA) pathway plays a crucial role in protecting animal germ cells by repressing transposons. However, the mechanism of piRNA-guided heterochromatin formation and its relationship to transcriptional termination remains elusive. Through RNA interference screening, we discovered Pcf11 and PNUTS as essential for piRNA-guided silencing in Drosophila germ line. Enforced tethering of Pcf11 leads to co-transcriptional repression and RNA polymerase II (RNA Pol II) stalling, and both are dependent on an α-helical region of Pcf11 capable of forming condensates. An intrinsically disordered region can substitute for the α-helical region of Pcf11 in its silencing capacity and support animal development, arguing for a causal relationship between phase separation and Pcf11's function. Pcf11 stalls RNA Pol II by preferentially forming condensates with the unphosphorylated Spt5, promoted by the PP1/PNUTS phosphatase during termination. We propose that Pcf11/Spt5 condensates control termination by decelerating polymerase elongation, a property exploited by piRNAs to silence transposons and initiate RNA-mediated heterochromatin formation.
    Keywords:  PNUTS/PP1; Pcf11; Spt5; condensate; heterochromatin; piRNA; termination; transposon
    DOI:  https://doi.org/10.1016/j.molcel.2025.01.023
  23. Proc Natl Acad Sci U S A. 2025 Mar 04. 122(9): e2418456122
    Linking DNA-packing density distribution and TAD boundary locations.
    Luming Meng, Fu Kit Sheong, Qiong Luo.
      DNA is heterogeneously packaged into chromatin, which is further organized into topologically associating domains (TADs) with sharp boundaries. These boundary locations are critical for genome regulation. Here, we explore how the distribution of DNA-packing density across chromatin affects the TAD boundary locations. We develop a polymer-physics-based model that utilizes DNA accessibility data to parameterize DNA-packing density along chromosomes, treating them as heteropolymers, and simulates the stochastic folding of these heteropolymers within a nucleus to yield a conformation ensemble. Such an ensemble reproduces a subset (over 60%) of TAD boundaries across the human genome, as confirmed by Hi-C data. Additionally, it reproduces the spatial distance matrices of 2-Mb genomic regions provided by FISH experiments. Furthermore, our model suggests that utilizing DNA accessibility data alone as input is sufficient to predict the emergence and disappearance of key TADs during early T cell differentiation. We show that stochastic folding of heteropolymers in a confined space can replicate both the prevalence of chromatin domain structures and the cell-to-cell variation in domain boundary positions observed in single-cell experiments. Furthermore, regions of lower DNA-packing density preferentially form domain boundaries, and this preference drives the emergence of TAD boundaries observed in ensemble-averaged Hi-C maps. The enrichment of TAD boundaries at CTCF binding sites can be attributed to the influence of CTCF binding on local DNA-packing density in our model. Collectively, our findings establish a strong link between TAD boundaries and regions of lower DNA-packing density, providing insights into the mechanisms underlying TAD formation.
    Keywords:  chromatin accessibility; early T cell differentiation; polymer physics model; topologically associating domains
    DOI:  https://doi.org/10.1073/pnas.2418456122
  24. Genes Dev. 2025 Feb 27.
    The transcription factor SRF regulates MERVL retrotransposons and gene expression during zygotic genome activation.
    Clara Hermant, Carlos Michel Mourra-Díaz, Marlies E Oomen, Luis Altamirano-Pacheco, Mrinmoy Pal, Tsunetoshi Nakatani, Maria-Elena Torres-Padilla.
      The regulatory circuitry of cell-specific transcriptional programs is thought to be influenced by transposable elements (TEs), whereby TEs serve as raw material for the diversification and genome-wide distribution of genetic elements that contain cis-regulatory activity. However, the transcriptional activators of TEs in relevant physiological contexts are largely unknown. Here, we undertook an evolutionary approach to identify regulators of two main families of MERVL, a major regulator of transcription during early mouse development. Using a combination of phyloregulatory, transcriptomic, and loss-of-function approaches, we demonstrate that SRF is a novel regulator of MERVL and embryonic transcription during zygotic genome activation. By resolving the phylogenetic history of two major MERVL families, we delineate the evolutionary acquisition of SRF and DUX binding sites and show that the acquisition of the SRF site precedes that of DUX. SRF contributes to embryonic transcription through the regulation of MERVLs, which in turn serve as promoters for host genes. Our work identifies new transcriptional regulators and TEs that shape the gene expression programs in early embryos and highlights the process of TE domestication via the sequential acquisition of transcription factor binding sites and coevolution with the host.
    Keywords:  MERVL; mouse embryos; retrotransposons; transcription
    DOI:  https://doi.org/10.1101/gad.352270.124
  25. Nat Commun. 2025 Feb 26. 16(1): 1999
    ETVs dictate hPSC differentiation by tuning biophysical properties.
    Natalia M Ziojła, Magdalena Socha, M Cecilia Guerra, Dorota Kizewska, Katarzyna Blaszczyk, Edyta Urbaniak, Sara Henry, Malgorzata Grabowska, Kathy K Niakan, Aryeh Warmflash, Malgorzata Borowiak.
      Stem cells maintain a dynamic dialog with their niche, integrating biochemical and biophysical cues to modulate cellular behavior. Yet, the transcriptional networks that regulate cellular biophysical properties remain poorly defined. Here, we leverage human pluripotent stem cells (hPSCs) and two morphogenesis models - gastruloids and pancreatic differentiation - to establish ETV transcription factors as critical regulators of biophysical parameters and lineage commitment. Genetic ablation of ETV1 or ETV1/ETV4/ETV5 in hPSCs enhances cell-cell and cell-ECM adhesion, leading to aberrant multilineage differentiation including disrupted germ-layer organization, ectoderm loss, and extraembryonic cell overgrowth in gastruloids. Furthermore, ETV1 loss abolishes pancreatic progenitor formation. Single-cell RNA sequencing and follow-up assays reveal dysregulated mechanotransduction via the PI3K/AKT signaling. Our findings highlight the importance of transcriptional control over cell biophysical properties and suggest that manipulating these properties may improve in vitro cell and tissue engineering strategies.
    DOI:  https://doi.org/10.1038/s41467-025-56591-6
  26. Dev Cell. 2025 Feb 24. pii: S1534-5807(25)00064-4. [Epub ahead of print]
    Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development.
    Shreeta Chakraborty, Nina Wenzlitschke, Matthew J Anderson, Ariel Eraso, Manon Baudic, Joyce J Thompson, Alicia A Evans, Lilly M Shatford-Adams, Raj Chari, Parirokh Awasthi, Ryan K Dale, Mark Lewandoski, Timothy J Petros, Pedro P Rocha.
      Chromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysregulation and phenotypes. We tested whether perturbing a domain with multiple developmental regulators would lead to more severe outcomes. We chose a domain with three FGF ligand genes-Fgf3, Fgf4, and Fgf15-that control different murine developmental processes. Heterozygous deletion of a 23.9-kb boundary defined by four CTCF sites led to ectopic interactions of the FGF genes with enhancers active in the brain and induced FGF expression. This caused orofacial clefts, encephalocele, and fully penetrant perinatal lethality. Loss of the single CTCF motif oriented toward the enhancers-but not the three toward the FGF genes-recapitulated these phenotypes. Our works shows that small sequence variants at particular domain boundaries can have a surprisingly outsized effect and must be considered as potential sources of gene dysregulation in development and disease.
    Keywords:  CTCF; FGF; epigenetics; gene regulation; nuclear organization
    DOI:  https://doi.org/10.1016/j.devcel.2025.02.002
  27. Genome Biol. 2025 Feb 26. 26(1): 41
    Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2.
    Henri Schmidt, Minsi Zhang, Dimitar Chakarov, Vineet Bansal, Haralambos Mourelatos, Francisco J Sánchez-Rivera, Scott W Lowe, Andrea Ventura, Christina S Leslie, Yuri Pritykin.
      We present GuideScan2 for memory-efficient, parallelizable construction of high-specificity CRISPR guide RNA (gRNA) databases and user-friendly design and analysis of individual gRNAs and gRNA libraries for targeting coding and non-coding regions in custom genomes. GuideScan2 analysis identifies widespread confounding effects of low-specificity gRNAs in published CRISPR screens and enables construction of a gRNA library that reduces off-target effects in a gene essentiality screen. GuideScan2 also enables the design and experimental validation of allele-specific gRNAs in a hybrid mouse genome. GuideScan2 will facilitate CRISPR experiments across a wide range of applications.
    Keywords:  Algorithm; Burrows-Wheeler transform; CRISPR; Guide RNA; GuideScan2; Off-targets; Software; Web interface
    DOI:  https://doi.org/10.1186/s13059-025-03488-8
  28. Elife. 2025 Feb 26. pii: RP94754. [Epub ahead of print]13
    Control of ciliary transcriptional programs during spermatogenesis by antagonistic transcription factors.
    Weihua Wang, Junqiao Xing, Xiqi Zhang, Hongni Liu, Xingyu Liu, Haochen Jiang, Cheng Xu, Xue Zhao, Zhangfeng Hu.
      Existence of cilia in the last eukaryotic common ancestor raises a fundamental question in biology: how the transcriptional regulation of ciliogenesis has evolved? One conceptual answer to this question is by an ancient transcription factor regulating ciliary gene expression in both uni- and multicellular organisms, but examples of such transcription factors in eukaryotes are lacking. Previously, we showed that an ancient transcription factor X chromosome-associated protein 5 (Xap5) is required for flagellar assembly in Chlamydomonas. Here, we show that Xap5 and Xap5-like (Xap5l) are two conserved pairs of antagonistic transcription regulators that control ciliary transcriptional programs during spermatogenesis. Male mice lacking either Xap5 or Xap5l display infertility, as a result of meiotic prophase arrest and sperm flagella malformation, respectively. Mechanistically, Xap5 positively regulates the ciliary gene expression by activating the key regulators including Foxj1 and Rfx families during the early stage of spermatogenesis. In contrast, Xap5l negatively regulates the expression of ciliary genes via repressing these ciliary transcription factors during the spermiogenesis stage. Our results provide new insights into the mechanisms by which temporal and spatial transcription regulators are coordinated to control ciliary transcriptional programs during spermatogenesis.
    Keywords:  Xap5; Xap5l; antagonistic transcription factors; cell biology; cilia; mouse; spermatogenesis; transcriptional regulation
    DOI:  https://doi.org/10.7554/eLife.94754
  29. Nat Commun. 2025 Feb 23. 16(1): 1900
    Pluripotency factor Tex10 finetunes Wnt signaling for spermatogenesis and primordial germ cell development.
    Feifei Yuan, Jihong Yang, Fanglin Ma, Zhe Hu, Vikas Malik, Ruge Zang, Dan Li, Xianle Shi, Xin Huang, Hongwei Zhou, Jianlong Wang.
      Testis-specific transcript 10 (Tex10) is highly expressed in the testis, embryonic stem cells (ESCs), and primordial germ cells (PGCs). We previously generated a Tex10 knockout mouse model demonstrating its critical roles in ESC pluripotency and preimplantation development. Here, using conditional knockout mice and dTAG-degron ESCs, we show Tex10 is required for spermatogenesis and ESC-to-PGCLC differentiation. Specifically, Tex10-null spermatocytes arrest at metaphase I, compromising round spermatid formation. Tex10 depletion and overexpression compromise and enhance ESC-to-PGCLC differentiation, respectively. Mechanistically, bulk and single-cell RNA sequencing reveals that Tex10 depletion downregulates genes involved in pluripotency, PGC development, and spermatogenesis while upregulating genes promoting somatic programs. Chromatin occupancy study reveals that Tex10 binds to H3K4me3-marked promoters of Psmd3 and Psmd7, negative regulators of Wnt signaling, and activates their expression, thereby restraining Wnt signaling. Our study identifies Tex10 as a previously unappreciated factor in spermatogenesis and PGC development, offering potential therapeutic insights for treating male infertility.
    DOI:  https://doi.org/10.1038/s41467-025-57165-2
  30. Nucleic Acids Res. 2025 Feb 08. pii: gkaf130. [Epub ahead of print]53(4):
    Rescuing DNMT1 fails to fully reverse the molecular and functional repercussions of its loss in mouse embryonic stem cells.
    Elizabeth Elder, Anthony Lemieux, Lisa-Marie Legault, Maxime Caron, Virginie Bertrand-Lehouillier, Thomas Dupas, Noël J-M Raynal, Guillaume Bourque, Daniel Sinnett, Nicolas Gévry, Serge McGraw.
      Epigenetic mechanisms are crucial for developmental programming and can be disrupted by environmental stressors, increasing susceptibility to disease. This has sparked interest in therapies for restoring epigenetic balance, but it remains uncertain whether disordered epigenetic mechanisms can be fully corrected. Disruption of DNA methyltransferase 1 (DNMT1), responsible for DNA methylation maintenance, has particularly devastating biological consequences. Therefore, here we explored if rescuing DNMT1 activity is sufficient to reverse the effects of its loss utilizing mouse embryonic stem cells. However, only partial reversal could be achieved. Extensive changes in DNA methylation, histone modifications, and gene expression were detected, along with transposable element derepression and genomic instability. Reduction of cellular size, complexity, and proliferation rate were observed, as well as lasting effects in germ layer lineages and embryoid bodies. Interestingly, by analyzing the impact on imprinted regions, we uncovered 20 regions exhibiting imprinted-like signatures. Notably, while many permanent effects persisted throughout Dnmt1 inactivation and rescue, others arose from the rescue intervention. Lastly, rescuing DNMT1 after differentiation initiation worsened outcomes, reinforcing the need for early intervention. Our findings highlight the far-reaching functions of DNMT1 and provide valuable perspectives on the repercussions of epigenetic perturbations during early development and the challenges of rescue interventions.
    DOI:  https://doi.org/10.1093/nar/gkaf130
  31. Cell Rep. 2025 Feb 18. pii: S2211-1247(25)00058-0. [Epub ahead of print]44(2): 115287
    Glycolytic reprogramming shapes the histone acetylation profile of activated CD4+ T cells in juvenile idiopathic arthritis.
    Enric Mocholi, Edward Corrigan, Theo Chalkiadakis, Can Gulersonmez, Edwin Stigter, Bas Vastert, Jorg van Loosdregt, Stefan Prekovic, Paul J Coffer.
      Juvenile idiopathic arthritis (JIA) is an autoimmune disease characterized by accumulation of activated CD4+ T cells in the synovial fluid (SF) of affected joints. JIA CD4+ T cells exhibit a unique inflammation-associated epigenomic signature, but the underlying mechanisms remain unclear. We demonstrate that CD4+ T cells from JIA SF display heightened glycolysis upon activation and JIA-specific H3K27 acetylation, driving transcriptional reprogramming. Pharmacological inhibition of glycolysis altered the expression of genes associated with these acetylated regions. Healthy CD4+ T cells exposed to JIA SF exhibited increased glycolytic activity and transcriptomic changes marked by heightened histone 3 lysine 27 acetylation (H3K27ac) at JIA-specific genes. Elevated H3K27ac was dependent on glycolytic flux, while inhibiting glycolysis or pyruvate dehydrogenase (PDH) impaired transcription of SF-driven genes. These findings demonstrate a key role of glycolysis in JIA-specific gene expression, offering potential therapeutic targets for modulating inflammation in JIA.
    Keywords:  CP: Immunology; CP: Metabolism; T cells; autoimmune disease; glucose metabolism; histone acetylation; juvenile idiopathic arthritis; pyruvate dehydrogenase
    DOI:  https://doi.org/10.1016/j.celrep.2025.115287
  32. Nat Commun. 2025 Feb 24. 16(1): 1939
    Maternal PRDM10 activates essential genes for oocyte-to-embryo transition.
    Michelle K Y Seah, Brenda Y Han, Yan Huang, Louise J H Rasmussen, Andrina J Stäubli, Judith Bello-Rodríguez, Andrew Chi-Ho Chan, Maxime Gasnier, Heike Wollmann, Ernesto Guccione, Daniel M Messerschmidt.
      PR/SET domain-containing (PRDM) proteins are metazoan-specific transcriptional regulators that play diverse roles in mammalian development and disease. Several members such as PRDM1, PRDM14 and PRDM9, have been implicated in germ cell specification and homoeostasis and are essential to fertility-related processes. Others, such as PRDM14, PRDM15 and PRDM10 play a role in early embryogenesis and embryonic stem cell maintenance. Here, we describe the first PRDM family member with a maternal effect. Absence of maternal Prdm10 results in catastrophic failure of oocyte-to-embryo transition and complete arrest at the 2-cell stage. We describe multiple defects in oocytes, zygotes and 2-cell stage embryos relating to the failure to accumulate PRDM10 target gene transcripts in the egg. Transcriptomic analysis and integration of genome-wide chromatin-binding data reveals new and essential PRDM10 targets, including the cytoskeletal protein encoding gene Septin11. We demonstrate that the failure to express maternal Septin11, in the absence of maternal PRDM10, disrupts Septin-complex assembly at the polar body extrusion site in MII oocytes. Our study sheds light into the essentiality of maternal PRDM10, the requirement of the maternal Septin-complex and the likely evolutionary conservation of this regulatory axis in human female germ cells.
    DOI:  https://doi.org/10.1038/s41467-025-56991-8
  33. Biochemistry. 2025 Feb 25.
    A Distinct Mechanism of RNA Recognition by the Transcription Factor GATA1.
    Daniella A Ugay, Robert T Batey, Deborah S Wuttke.
      Several human transcription factors (TFs) have been reported to directly bind RNA through noncanonical RNA-binding domains; however, most of these TFs remain to be further validated as bona fide RNA-binding proteins (RBPs). Our systematic analysis of RBP discovery data sets reveals a varied set of candidate TF-RBPs that encompass most TF families. These candidate RBPs include members of the GATA family that are essential factors in embryonic development. Investigation of the RNA-binding features of GATA1, a major hematopoietic TF, reveals robust sequence independent binding to RNAs in vitro. Moreover, RNA binding by GATA1 is competitive with DNA binding, which occurs through a shared binding surface spanning the DNA-binding domain and arginine-rich motif (ARM)-like domain. We show that the ARM-like domain contributes substantially to high-affinity DNA binding and electrostatically to plastic RNA recognition, suggesting that the separable RNA-binding domain assigned to the ARM-domain in GATA1 is an oversimplification of a more complex recognition network. These biochemical data demonstrate a unified integration of DNA- and RNA-binding surfaces within GATA1, whereby the ARM-like domain provides an electrostatic surface for RNA binding but does not fully dominate GATA1-RNA interactions, which may also apply to other TF-RBPs. This competitive DNA/RNA binding activity using overlapping nucleic acid binding regions points to the possibility of RNA-mediated regulation of the GATA1 function during hematopoiesis. Our study highlights the multifunctionality of DNA-binding domains in RNA recognition and supports the need for robust characterization of predicted noncanonical RNA-binding domains such as ARM-like domains.
    DOI:  https://doi.org/10.1021/acs.biochem.4c00818
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