bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2025–06–15
27 papers selected by
Connor Rogerson, University of Cambridge
  1. Cohesin stabilization at promoters and enhancers by common transcription factors and chromatin regulators.
  2. Chip (Ldb1) is a putative cofactor of Zelda forming a functional bridge to CBP during zygotic genome activation.
  3. Bulk-level maps of pioneer factor binding dynamics during Drosophila maternal-to-zygotic transition.
  4. Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts.
  5. Opposing lineage specifiers induce a protumor hybrid identity state in lung adenocarcinoma.
  6. Mitotic chromosomes harbor cell type and species-specific structural features within a universal loop array conformation.
  7. Transcription factor binding divergence drives transcriptional and phenotypic variation in maize.
  8. Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC.
  9. Synaptic activity causes minute-scale changes in BAF complex composition and function.
  10. Small DNA elements can act as both insulators and silencers in plants.
  11. In vivo transition in chromatin accessibility during differentiation of deep-layer excitatory neurons in the neocortex.
  12. Engineered transcription factor-binding arrays for DNA-based gene expression control in mammalian cells.
  13. CREPT is required for the metastasis of triple-negative breast cancer through a co-operational-chromatin loop-based gene regulation.
  14. Genome-wide identification and analysis of recurring patterns of epigenetic variation across individuals.
  15. Pioneer factor ETV2 safeguards endothelial cell specification by recruiting the repressor REST to restrict alternative lineage commitment.
  16. Mutant EZH2 alters the epigenetic network and increases epigenetic heterogeneity in B cell lymphoma.
  17. Cell states and neighborhoods in distinct clinical stages of primary and metastatic esophageal adenocarcinoma.
  18. Uncovering candidate Nanog-Helper genes in early mouse embryo differentiation using differential entropy and network inference.
  19. The transcription factor IID subunit Taf13 is dispensable for TATA binding protein promoter recruitment and RNA polymerase II transcription.
  20. Regulation of epigenetics and chromosome structure by human ORC2.
  21. Decoding gene networks controlling hypothalamic and prethalamic neuron development.
  22. Spatial organization, chromatin accessibility and gene-regulatory programs defining mouse sensory neurons.
  23. Ligand-specific regulation of a binary enhancer code dictating cellular senescence.
  24. Super-enhancer-mediated circRNAs exhibit high splicing circularization diversity and transcriptional activity.
  25. MINGLE: a mutual information-based interpretable framework for automatic cell type annotation in single-cell chromatin accessibility data.
  26. Combinatorial transcriptional regulation establishes subtype-appropriate synaptic properties in auditory neurons.
  27. Vostok: A looping factor for the organization of the regulatory genome in the Drosophila brain.
  1. Epigenetics Chromatin. 2025 Jun 09. 18(1): 33
    Cohesin stabilization at promoters and enhancers by common transcription factors and chromatin regulators.
    Audra F Bryan, Megan Justice, Alexis V Stutzman, Daniel J McKay, Jill M Dowen.
       BACKGROUND: Cohesin is a major regulator of three-dimensional genome organization and gene expression. Cohesin associates with DNA and dynamically extrudes a DNA loop, often bringing two cis-regulatory elements physically close together. Extruding cohesin molecules can be stalled or stabilized when they encounter a CTCF insulator protein on DNA, thereby anchoring a DNA loop. However, many enhancer-promoter loops that are bound by cohesin lack CTCF and it is not clear how cohesin is stabilized at or recruited to these sites in the genome.
    RESULTS: Here, we investigated the localization of cohesin with common chromatin regulators and transcription factors on the mouse embryonic stem cell genome. The SP1 and NFYA transcription factors are ubiquitously expressed proteins known to regulate expression of genes associated with a variety of cellular processes, while WDR5 is a ubiquitous core component of multiple chromatin regulatory complexes. We found that cohesin co-bound promoters and enhancers with WDR5, with SP1, or with NFYA in mESCs. Cohesin physically interacted with and colocalized with WDR5, with SP1, or with NFYA on the same molecule of chromatin. Strikingly, depletion of WDR5, SP1, or NFYA caused a decrease in cohesin binding at shared binding sites, while depletion of cohesin did not alter binding of WDR5, SP1, or NFYA on the genome.
    CONCLUSIONS: These results indicate that common transcription factors and chromatin regulators stabilize cohesin at specific sites in chromatin and may thereby serve as structural regulators of enhancer-promoter loops via the stabilization of cohesin.
    Keywords:  Chromatin; Cohesin; Enhancer; NFYA; Promoter; SP1; Transcription; WDR5
    DOI:  https://doi.org/10.1186/s13072-025-00598-2
  2. Mol Cell. 2025 Jun 05. pii: S1097-2765(25)00457-5. [Epub ahead of print]
    Chip (Ldb1) is a putative cofactor of Zelda forming a functional bridge to CBP during zygotic genome activation.
    Charalampos Chrysovalantis Galouzis, Yacine Kherdjemil, Mattia Forneris, Rebecca R Viales, Raquel Marco-Ferreres, Eileen E M Furlong.
      The cofactor LIM-domain-binding protein 1 (Ldb1) is linked to many processes in gene regulation, including enhancer-promoter communication, interchromosomal interactions, and enhanceosome-cofactor-like activity. However, its functional requirement and molecular role during embryogenesis remain unclear. Here, we used optogenetics (iLEXY) to rapidly deplete Drosophila Ldb1 (Chip) from the nucleus at precise time windows. Remarkably, this pinpointed the essential window of Chip's function to just 1 h of embryogenesis, overlapping zygotic genome activation (ZGA). We show that Zelda, a pioneer factor essential for ZGA, recruits Chip to chromatin, and both factors regulate concordant changes in gene expression, suggesting that Chip is a cofactor of Zelda. Chip does not significantly impact chromatin architecture at these stages, but instead recruits CBP, and is essential for H3K27ac deposition at enhancers and promoters, and for the proper expression of co-regulated genes. These data identify Chip as a functional bridge between Zelda and the coactivator CBP to regulate gene expression in early embryogenesis.
    Keywords:  CBP; cofactors; developmental enhancers; embryogenesis; transcription factors; transcriptional regulation; zygotic genome activation
    DOI:  https://doi.org/10.1016/j.molcel.2025.05.018
  3. Development. 2025 Jun 13. pii: dev.204460. [Epub ahead of print]
    Bulk-level maps of pioneer factor binding dynamics during Drosophila maternal-to-zygotic transition.
    Sadia Siddika Dima, Gregory T Reeves.
      Gene regulation by transcription factors (TFs) binding cognate sequences is of paramount importance. For example, the TFs Zelda (Zld) and GAGA factor (GAF) are widely acknowledged for pioneering gene activation during zygotic genome activation (ZGA) in Drosophila. However, quantitative dose/response relationships between bulk TF concentration and DNA binding, an event tied to transcriptional activity, remain elusive. Here, we map these relationships during ZGA: a crucial step in metazoan development. To map the dose/response relationship between nuclear concentration and DNA binding, we performed raster image correlation spectroscopy, a method that can measure biophysical parameters of fluorescent molecules. We found that, although Zld concentration increases during nuclear cycles (ncs) 10 to 14, its binding in the transcriptionally active regions decreases, consistent with its function as an activator for early genes. In contrast, GAF-DNA binding is nearly linear with its concentration, which sharply increases during the major wave, implicating it in the major wave. This study provides key insights into the properties of the two factors and puts forward a quantitative approach that can be used for other TFs to study transcriptional regulation.
    Keywords:  DNA binding; GAGA factor; Pioneer factors; Raster image correlation spectroscopy; Zelda; Zygotic genome activation
    DOI:  https://doi.org/10.1242/dev.204460
  4. Genome Res. 2025 Jun 10.
    Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts.
    Yanis Zekri, Sebastian Gregoricchio, Elif Yapıcı, Chia-Chi Flora Huang, Tunç Morova, Umut Berkay Altıntaş, Gozde Korkmaz, Nathan A Lack, Wilbert Zwart.
      Estrogen receptor 1 (ESR1; also known as ERα, encoded by ESR1 gene) is the driving transcription factor in breast cancer development and progression. ESR1 genomic action is thought to operate under tight epigenetic control, with its chromatin binding and subsequent transcriptional output heavily reliant on the pioneer transcription factor FOXA1, which renders chromatin accessible for ESR1 binding. However, the exact contribution of the epigenome to selective enhancer activation by ESR1 remains to be fully elucidated. To address this, we employ a massively parallel reporter assay to profile 7576 individual ESR1 binding sites for hormone responsiveness. Only a minority of ESR1-occupied enhancers exhibit hormone-induced activity. These findings are confirmed by genomic data in situ, indicating that enhancer activation within a chromatinized context is robustly captured in a plasmid-based reporter assay. In silico integration of our findings with publicly available functional genomics data sets from breast cancer cell lines and tumor samples reveal distinct transcription complex compositions, 3D genome contexts, and regulatory dynamics associated with different classes of ESR1 binding sites. Overall, our results establish a comprehensive framework to highlight and elucidate the molecular basis underlying ESR1 genomic heterogeneity and its contribution to breast cancer biology and clinical outcomes.
    DOI:  https://doi.org/10.1101/gr.280320.124
  5. Genes Dev. 2025 Jun 12.
    Opposing lineage specifiers induce a protumor hybrid identity state in lung adenocarcinoma.
    Gabriela Fort, Henry Arnold, Soledad A Camolotto, Kayla O'Toole, Rushmeen Tariq, Anna Waters, Katherine Gillis, Eric L Snyder.
      Lineage plasticity is critical for tumor progression and therapy resistance, but the molecular mechanisms underlying cell identity shifts in cancer remain poorly understood. In lung adenocarcinoma (LUAD), the loss of pulmonary lineage fidelity and acquisition of alternate identity programs converge on hybrid identity (hybrid ID) states, which are postulated to be key intermediates in LUAD evolution and are characterized by the coactivation of developmentally incompatible identity programs within individual cells. Here, we uncover a previously unrecognized role for the gastrointestinal transcriptional regulator HNF4α in driving tumor growth and hybrid ID states in LUAD. In LUAD cells expressing the lung lineage specifier NKX2-1, HNF4α induces a GI/liver-like state by directly binding and activating its canonical targets. HNF4α also disrupts NKX2-1 genomic localization and dampens pulmonary identity within hybrid ID LUAD. We show that this hybrid ID state is maintained by sustained RAS/MEK signaling. Inhibition of the RAS/MEK signaling cascade augments NKX2-1 chromatin binding at pulmonary-specific genes and induces drug resistance-associated pulmonary signatures. Finally, we demonstrate that HNF4α depletion sensitizes LUAD cells to KRASG12D inhibition. Collectively, our data show that coexpression of opposing lineage specifiers is a novel mechanism of identity dysregulation in LUAD that influences both tumor progression and response to targeted therapy.
    Keywords:  KRAS inhibition; hybrid identity; lineage plasticity; lineage specifiers; lung adenocarcinoma
    DOI:  https://doi.org/10.1101/gad.352742.125
  6. Genome Res. 2025 Jun 06. pii: gr.280648.125. [Epub ahead of print]
    Mitotic chromosomes harbor cell type and species-specific structural features within a universal loop array conformation.
    Marlies E Oomen, A Nicole Fox, Inma Gonzalez, Amandine Molliex, Thaleia Papadopoulou, Pablo Navarro, Job Dekker.
      Mitotic chromosomes are considered to be universally folded as loop arrays across species and cell types. However, some studies suggest that features of mitotic chromosomes might be cell type or species specific. We previously reported that CTCF binding in human differentiated cell lines is lost in mitosis, whereas mitotic mouse embryonic stem cells (mESC) display prominent binding at a subset of CTCF sites. Here, we perform footprint ATAC-seq analyses of mESCs and somatic mouse and human cells confirming these findings. We then investigate roles of mitotically bookmarked CTCF in prometaphase chromosome organization by Hi-C. We do not find any remaining interphase structures such as TADs or loops at bookmarked CTCF sites in mESCs. This suggests that mitotic loop extruders condensin I and II are not blocked by CTCF, and thus that maintained CTCF binding does not alter mitotic chromosome folding. Lastly, we compare mitotic Hi-C data generated in this study in mouse with public data in human and chicken. We do not find any cell type-specific differences; however, we find a difference between species. The average genomic size of mitotic loops is smaller in chicken (200-300 kb), compared to human (400-600 kb) and especially mouse (1-1.5 mb). Interestingly, we find that this difference is correlated with the genomic length of q-arms in these species, a finding we confirm by microscopy measurements of chromosome compaction. This suggests that the dimensions of mitotic chromosomes can be modulated through control of loop size by condensins to facilitate species-appropriate shortening of chromosome arms.
    DOI:  https://doi.org/10.1101/gr.280648.125
  7. Nat Plants. 2025 Jun 12.
    Transcription factor binding divergence drives transcriptional and phenotypic variation in maize.
    Mary Galli, Zongliang Chen, Tara Ghandour, Amina Chaudhry, Jason Gregory, Fan Feng, Miaomiao Li, Nathaniel Schleif, Xuan Zhang, Yinxin Dong, Gaoyuan Song, Justin W Walley, George Chuck, Clinton Whipple, Heidi F Kaeppler, Shao-Shan Carol Huang, Andrea Gallavotti.
      Regulatory elements are essential components of plant genomes that have shaped the domestication and improvement of modern crops. However, their identity, function and diversity remain poorly characterized, limiting our ability to harness their full power for agricultural advances using induced or natural variation. Here we mapped transcription factor (TF) binding for 200 TFs from 30 families in two distinct maize inbred lines historically used in maize breeding. TF binding comparison revealed widespread differences between inbreds, driven largely by structural variation, that correlated with gene expression changes and explained complex quantitative trait loci such as Vgt1, an important determinant of flowering time, and DICE, an herbivore resistance enhancer. CRISPR-Cas9 editing of TF binding regions validated the function and structure of regulatory regions at various loci controlling plant architecture and biotic resistance. Our maize TF binding catalogue identifies functional regulatory regions and enables collective and comparative analysis, highlighting its value for agricultural improvement.
    DOI:  https://doi.org/10.1038/s41477-025-02007-8
  8. Nat Commun. 2025 Jun 10. 16(1): 5136
    Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC.
    Songlei Liu, Li Li, Fan Zhang, Mariana Garcia-Corral, Katharina Meyer, Patrick R J Fortuna, Björn van Sambeek, Evan Appleton, Alex H M Ng, Parastoo Khoshakhlagh, Yuancheng Ryan Lu, James Cameron, Ricardo N Ramirez, Yuting Chen, Chun-Ting Wu, Jeremy Y Huang, Yuqi Tan, George Chao, John Aach, Elaine T Lim, Jenny M Tam, Soumya Raychaudhuri, George M Church.
      Differentiation of induced pluripotent stem cells (iPSCs) into specialized cell types is essential for uncovering cell-type specific molecular mechanisms and interrogating cellular function. Transcription factor screens have enabled efficient production of a few cell types; however, engineering cell types that require complex transcription factor combinations remains challenging. Here, we report an iterative, high-throughput single-cell transcription factor screening method that enables the identification of transcription factor combinations for specialized cell differentiation, which we validated by differentiating human microglia-like cells. We found that the expression of six transcription factors, SPI1, CEBPA, FLI1, MEF2C, CEBPB, and IRF8, is sufficient to differentiate human iPSC into cells with transcriptional and functional similarity to primary human microglia within 4 days. Through this screening method, we also describe a novel computational method allowing the exploration of single-cell RNA sequencing data derived from transcription factor perturbation assays to construct causal gene regulatory networks for future cell fate engineering.
    DOI:  https://doi.org/10.1038/s41467-025-59596-3
  9. Mol Cell. 2025 Jun 03. pii: S1097-2765(25)00456-3. [Epub ahead of print]
    Synaptic activity causes minute-scale changes in BAF complex composition and function.
    Sai Gourisankar, Sabin A Nettles, Wendy Wenderski, Joao A Paulo, Sam H Kim, Kyra C Roepke, Claire Ellis, Hind Z Abuzaid, Steven P Gygi, Gerald R Crabtree.
      Genes encoding subunits of the BAF ATP-dependent chromatin remodeling complex are among the most enriched for deleterious de novo mutations in intellectual disabilities and autism spectrum disorder, but the causative molecular pathways are not understood. Synaptic activity in neurons is critical for learning, memory, and proper neural development. While BAF is required for activity-dependent developmental processes, such as dendritic outgrowth, the immediate molecular consequences of neuronal activity on BAF complexes are unknown. Here, we report that neuronal activity induces dramatic remodeling of the subunit composition of BAF complexes within 15 min, concurrent with both phosphorylation and dephosphorylation of its subunits. These biochemical effects are a convergent phenomenon downstream of multiple calcium-activated signaling pathways in mouse neurons and mouse fibroblasts and correspond to changes in BAF-dependent chromatin accessibility. Our studies imply that BAF decodes signals at the membrane by altering the combinatorial composition of its subunits.
    Keywords:  ATP-dependent chromatin remodeling; BAF (mSWI/SNF) complex; PBAF; activity-regulated transcription; chromatin accessibility; excitatory stimuli; neuron; polybromo-BAF; proteomics; synaptic activity
    DOI:  https://doi.org/10.1016/j.molcel.2025.05.017
  10. Plant Cell. 2025 Jun 04. pii: koaf084. [Epub ahead of print]37(6):
    Small DNA elements can act as both insulators and silencers in plants.
    Tobias Jores, Nicholas A Mueth, Jackson Tonnies, Si Nian Char, Bo Liu, Valentina Grillo-Alvarado, Shane Abbitt, Ajith Anand, Stéphane Deschamps, Scott Diehn, Bill Gordon-Kamm, Shuping Jiao, Kathy Munkvold, Heather Snowgren, Nagesh Sardesai, Stanley Fields, Bing Yang, Josh T Cuperus, Christine Queitsch.
      Insulators are cis-regulatory elements that separate transcriptional units, whereas silencers are elements that repress transcription regardless of their position. In plants, these elements remain largely uncharacterized. Here, we use the massively parallel reporter assay Plant STARR-seq with short fragments of 8 large insulators to identify more than 100 fragments that block enhancer activity. The short fragments can be combined to generate more powerful insulators that abolish the capacity of the strong viral 35S enhancer to activate the 35S minimal promoter. Unexpectedly, when tested upstream of weak enhancers, these fragments act as silencers and repress transcription. Thus, these elements are capable of insulating or repressing transcription, depending on the regulatory context. We validate our findings in stable transgenic Arabidopsis thaliana, maize (Zea mays), and rice (Oryza sativa) plants. The short elements identified here should be useful building blocks for plant biotechnology.
    DOI:  https://doi.org/10.1093/plcell/koaf084
  11. Development. 2025 Jun 12. pii: dev.204564. [Epub ahead of print]
    In vivo transition in chromatin accessibility during differentiation of deep-layer excitatory neurons in the neocortex.
    Seishin Sakai, Yurie Maeda, Mai Saeki, Daijiro Konno, Keita Kawaji, Fumio Matsuzaki, Yutaka Suzuki, Yukiko Gotoh, Yusuke Kishi.
      During neuronal differentiation, gene transcription patterns change in response to both intrinsic and extrinsic cues. Chromatin regulation at regulatory elements plays a key role in this process. However, how chromatin accessibility evolves in vivo in cortical neurons remains unclear. Here, we established a method for labeling differentiating neurons with specific birthdates. Using this method, we traced the four-day differentiation process of in vivo deep-layer excitatory neurons in the mouse embryonic cortex and examined changes in the genome-wide transcription pattern and chromatin accessibility using RNA-sequencing and DNase-sequencing, respectively. We found that genomic regions of genes linked to mature neuronal functions, including deep-layer-specific and stimulus-responsive genes, became accessible even at the embryonic stage. Additionally, our results indicated the involvement of bivalent marks in neural precursor/stem cells and Dmrt3 and Dmrta2 in regulating chromatin accessibility during neuronal differentiation. These findings highlight the importance of chromatin regulation in embryonic neurons, enabling the timely activation of neuronal genes during maturation.
    Keywords:  Bivalent genes; Chromatin accessibility; Cortical neurons; Differentiation; Dmrt; Transcriptome
    DOI:  https://doi.org/10.1242/dev.204564
  12. Trends Biotechnol. 2025 Jun 09. pii: S0167-7799(25)00172-6. [Epub ahead of print]
    Engineered transcription factor-binding arrays for DNA-based gene expression control in mammalian cells.
    Annalise Zouein, Brittany Lende-Dorn, Kate E Galloway, Tom Ellis, Francesca Ceroni.
      Tools that manipulate gene expression in mammalian cells without any additional expression are critical for cell engineering applications. Here, we demonstrate the use of arrays of transcription factor (TF) recognition elements (REs) as DNA tools for controlling gene expression. We first demonstrate that TetR-based RE arrays can alter synthetic gene circuit performance. We then open the approach to any TF with a known binding site by developing a new technique called Cloning Troublesome Repeats in Loops (CTRL), which can assemble plasmids with up to 256 RE repeats. Transfection of custom RE array plasmids assembled by CTRL into mammalian cells modifies host cell gene regulation by sequestration of TFs of interest and can sequester both synthetic and native TFs, offering applications in the control of gene circuits and for directing cell fate. This work advances our ability to assemble repetitive DNA arrays and shows how TF-binding RE arrays expand possibilities in mammalian cell engineering.
    Keywords:  gene expression regulation; mammalian cells; synthetic biology; transcription factor; transcription factor decoy
    DOI:  https://doi.org/10.1016/j.tibtech.2025.05.006
  13. Mol Cancer. 2025 Jun 10. 24(1): 170
    CREPT is required for the metastasis of triple-negative breast cancer through a co-operational-chromatin loop-based gene regulation.
    Jianghua Li, Lu Xu, Jiayu Wang, Xuning Wang, Yuting Lin, Alex Yutian Zou, Fangli Ren, Yinyin Wang, Jun Li, Zhijie Chang.
      Triple-negative breast cancer (TNBC) is recognized for its aggressiveness, yet the mechanism underlying metastasis remains unclear. Here, we report that CREPT/RPRD1B, which exhibits somatic gene copy-number amplifications and elevated expression, correlates with poor patient survival and drives TNBC metastasis. We demonstrate that CREPT alters three-dimensional genome structures in topologically-associating domain (TAD) status and chromatin loops via occupying promoters and enhancers. Specifically, CREPT mediates 1082 co-operational chromatin loops configured by enhancer-promoter and promoter-termination loops, which are validated by HiChIP analyses and visualized by Tn5-FISH experiments. These loops orchestrate RNAPII loading and recycling to enhance the metastatic gene expression. Disruption of these co-operational loops using CRISPR-dCas9 suppresses TNBC metastasis in vivo. Furthermore, depletion of CREPT using an AAV-based shRNA blocks TNBC metastasis in both preventative and therapeutic mouse models. We propose that targeting CREPT to disrupt the co-operational chromatin loop structures represents a promising therapeutic strategy for metastatic TNBC.
    DOI:  https://doi.org/10.1186/s12943-025-02361-3
  14. Commun Biol. 2025 Jun 07. 8(1): 888
    Genome-wide identification and analysis of recurring patterns of epigenetic variation across individuals.
    Jennifer Zou, Emily Maciejewski, Jason Ernst.
      Epigenetic mapping studies across individuals have identified many positions of epigenetic variation across the human genome. However the relationships between these positions, and in particular global patterns that recur in many regions of the genome, remains understudied. In this study, we use a stacked chromatin state model to systematically learn global patterns of epigenetic variation across individuals and annotate the human genome based on them. We apply this framework to histone modification data across individuals in lymphoblastoid cell lines and across autism spectrum disorder cases and controls in prefrontal cortex tissue. We find that global patterns are correlated across multiple histone modifications and with gene expression. We use the global patterns as a framework to predict trans-regulators and study a complex disorder. The frameworks for identifying and analyzing global patterns of epigenetic variation are general and we expect will be useful in other systems.
    DOI:  https://doi.org/10.1038/s42003-025-08179-5
  15. Nat Cardiovasc Res. 2025 Jun 10.
    Pioneer factor ETV2 safeguards endothelial cell specification by recruiting the repressor REST to restrict alternative lineage commitment.
    Danyang Chen, Xiaonuo Fan, Ninghe Sun, Kai Wang, Liyan Gong, Juan M Melero-Martin, William T Pu.
      Mechanisms of cell fate specification are central to developmental biology and regenerative medicine. ETV2 is a master regulator for the endothelial cell (EC) lineage specification. Here we study mechanisms by which ETV2 overexpression in human induced pluripotent stem-cell-derived mesodermal progenitors efficiently specifies ECs. We used CUT&RUN, scRNA-seq and scATAC-seq to characterize the molecular features of EC differentiation mediated by ETV2. We defined the scope of ETV2 pioneering activity and identified its direct downstream target genes. Induced ETV2 expression both directed specification of endothelial progenitors and suppressed acquisition of alternative fates. Functional screening and candidate validation revealed cofactors essential for efficient EC specification, including the transcriptional activator GABPA. Notably, the transcriptional repressor REST was also necessary for efficient EC specification. ETV2 recruited REST to repress non-EC lineage genes. Our study provides an unparalleled molecular analysis of EC specification at single-cell resolution and highlights the important role of pioneer factors to recruit repressors that suppress commitment to alternative lineages.
    DOI:  https://doi.org/10.1038/s44161-025-00660-y
  16. PLoS Biol. 2025 Jun;23(6): e3003191
    Mutant EZH2 alters the epigenetic network and increases epigenetic heterogeneity in B cell lymphoma.
    Ofir Griess, Noa Furth, Nofar Harpaz, Nicoletta Di Bernardo, Tomer-Meir Salame, Bareket Dassa, Ioannis Karagiannidis, Yusuke Isshiki, Menachem Gross, Ari M Melnick, Wendy Béguelin, Guy Ron, Efrat Shema.
      Diffuse large B cell lymphomas and follicular lymphomas show recurrent mutations in epigenetic regulators; among these are loss-of-function mutations in KMT2D and gain-of-function mutations in EZH2. To systematically explore the effects of these mutations on the wiring of the epigenetic network, we applied a single-cell approach to probe a wide array of histone modifications. We show that mutant-EZH2 elicits extensive effects on the epigenome of lymphomas, beyond alterations to H3K27 methylations, and is epistatic over KMT2D mutations. Utilizing the single-cell data, we present computational methods to measure epigenetic heterogeneity. We identify an unexpected characteristic of mutant-EZH2, but not KMT2D, in increasing heterogeneity, shedding light on a novel oncogenic mechanism mediated by this mutation. Finally, we present tools to reconstruct known interactions within the epigenetic network, as well as reveal potential novel cross talk between various modifications, supported by functional perturbations. Our work highlights novel roles for mutant-EZH2 in lymphomagenesis and establishes new concepts for measuring epigenetic heterogeneity and intra-chromatin connectivity in cancer cells.
    DOI:  https://doi.org/10.1371/journal.pbio.3003191
  17. Cell Rep Med. 2025 Jun 03. pii: S2666-3791(25)00261-7. [Epub ahead of print] 102188
    Cell states and neighborhoods in distinct clinical stages of primary and metastatic esophageal adenocarcinoma.
    Josephine Yates, Camille Mathey-Andrews, Jihye Park, Amanda Garza, Andréanne Gagné, Samantha Hoffman, Kevin Bi, Breanna Titchen, Connor Hennessey, Joshua Remland, Matthew Carnes, Erin Shannon, Sabrina Camp, Siddhi Balamurali, Shweta Kiran Cavale, Zhixin Li, Akhouri Kishore Raghawan, Agnieszka Kraft, Genevieve Boland, Andrew J Aguirre, Nilay S Sethi, Valentina Boeva, Eliezer M Van Allen.
      Esophageal adenocarcinoma (EAC) is a highly lethal cancer of the upper gastrointestinal tract with rising incidence in western populations. To decipher EAC disease progression and therapeutic response, we perform multiomic analyses of a cohort of primary and metastatic EAC tumors, incorporating single-nuclei transcriptomic and chromatin accessibility sequencing along with spatial profiling. We recover tumor microenvironmental features previously described to associate with therapy response. We subsequently identify five malignant cell programs, including undifferentiated, intermediate, differentiated, epithelial-to-mesenchymal transition, and cycling programs, which are associated with differential epigenetic plasticity and clinical outcomes, and for which we infer candidate transcription factor regulons. Furthermore, we reveal diverse spatial localizations of malignant cells expressing their associated transcriptional programs and predict their significant interactions with microenvironmental cell types. We validate our findings in three external single-cell RNA sequencing (RNA-seq) and three bulk RNA-seq studies. Altogether, our findings advance the understanding of EAC heterogeneity, disease progression, and therapeutic response.
    Keywords:  bioinformatics; computational biology; epigenetics; esophageal adenocarcinoma; gastrointestinal cancer; oncology; single cell; spatial transcriptomics; transcriptomics
    DOI:  https://doi.org/10.1016/j.xcrm.2025.102188
  18. Sci Rep. 2025 Jun 06. 15(1): 19975
    Uncovering candidate Nanog-Helper genes in early mouse embryo differentiation using differential entropy and network inference.
    Francisco Prista von Bonhorst, Olivier Gandrillon, Ulysse Herbach, Corentin Robert, Claire Chazaud, Yannick De Decker, Didier Gonze, Geneviève Dupont.
      In the preimplantation mammalian embryo, stochastic cell-to-cell expression heterogeneity is followed by signal reinforcement to initiate the specification of Inner Cell Mass (ICM) cells into Epiblast (Epi). The expression of NANOG, the key transcription factor for the Epi fate, is necessary but not sufficient: coincident expression of other factors is required. To identify possible Nanog-helper genes, we analyzed gene expression variability in five time-stamped single-cell transcriptomic datasets using differential entropy, a quantitative measure of cell-to-cell heterogeneity. The entropy of Nanog displays a peak-shaped temporal pattern from the 16-cell to the 64-cell stage, consistent with its key role in Epi specification. By estimating the entropy profiles of the 21 genes common to all five datasets, we identified three genes - Pecam1, Sox2, and Hnf4a - whose variability in expression patterns mirrors that of Nanog. We further performed gene regulatory network inference using CARDAMOM, an algorithm that exploits temporal dynamics and transcriptional bursting. The results revealed that these three genes exhibit reciprocal activation with Nanog at the 32-cell stage. This regulatory motif reinforces fate-switching decisions and co-expression states. Our innovative analysis of single-cell transcriptomic data thus uncovers a likely role for Pecam1, Sox2, and Hnf4a as key genes that, when coincidentally expressed with Nanog, initiate ICM differentiation.
    DOI:  https://doi.org/10.1038/s41598-025-03956-y
  19. iScience. 2025 Jun 20. 28(6): 112286
    The transcription factor IID subunit Taf13 is dispensable for TATA binding protein promoter recruitment and RNA polymerase II transcription.
    Igor Martianov, Stephanie Le Gras, Guillaume Davidson, Irwin Davidson.
      The multiprotein complex TFIID, comprising the TATA binding protein (TBP) and 13 TBP-associated factors (TAFs), is an essential component of the RNA polymerase II (Pol II) preinitiation complex (PIC). Cryo-electron microscopy studies suggested a critical role of the TAF11-TAF13 heterodimer in TBP promoter deposition upstream of the transcription start site. To investigate this hypothesis, we inactivated the gene encoding Taf13 in mice and embryonic stem cells (ESCs). Taf13-null embryos implant and survive until E6.5, but fail to undergo gastrulation, while Taf13-null ESCs are viable, but fail to form embryoid bodies and differentiate. Taf13 loss had little effect on TFIID integrity and led to only a mild reduction of TBP promoter recruitment, but led to altered PIC formation and globally reduced Pol II recruitment. Thus, the Taf11-Taf13 heterodimer is not essential for TBP/TFIID recruitment, revealing plasticity in the pathways of PIC formation.
    Keywords:  Biochemistry; Developmental biology; Embryology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2025.112286
  20. Cell Rep. 2025 Jun 10. pii: S2211-1247(25)00587-X. [Epub ahead of print]44(6): 115816
    Regulation of epigenetics and chromosome structure by human ORC2.
    Zhangli Su, Mengxue Tian, Etsuko Shibata, Yoshiyuki Shibata, Tianyi Yang, Zhenjia Wang, Fulai Jin, Chongzhi Zang, Anindya Dutta.
      We report a multi-omics study in a human cell line with mutations in three subunits of origin-recognition complex (ORC). Although the ORC subunits should bind DNA as part of a common six-subunit ORC, there are thousands of sites in the genome where one subunit binds but not another. DNA-bound ORC2 compacts chromatin and attracts repressive histone marks to focal areas of the genome, but ORC2 also activates chromatin at many sites and protects the genes from repressive marks. These epigenetic changes regulate hundreds of genes, including some epigenetic regulators, adding an indirect mechanism by which ORC2 regulates epigenetics without local binding. DNA-bound ORC2 also prevents the acquisition of CTCF at focal sites in the genome to regulate chromatin loops and indirectly affect epigenetics. Thus, individual ORC subunits may bind to DNA to act as epigenetic and chromosome structure regulators independent of the role of the six-subunit ORC in DNA replication.
    Keywords:  CP: Genomics; CP: Molecular biology; CTCF; DNA replication; Hi-C; ORC; epigenetics; gene regulation; genomics; higher-order chromatin organization; histone modifications; origin-recognition complex
    DOI:  https://doi.org/10.1016/j.celrep.2025.115816
  21. Cell Rep. 2025 Jun 12. pii: S2211-1247(25)00629-1. [Epub ahead of print]44(6): 115858
    Decoding gene networks controlling hypothalamic and prethalamic neuron development.
    Dong Won Kim, Leighton H Duncan, Zheng Xu, Minzi Chang, Sara Sejer, Chantelle E Terrillion, Patrick O Kanold, Elsie Place, Seth Blackshaw.
      The hypothalamus and prethalamus regulate diverse physiological and behavioral processes, yet the gene regulatory networks guiding their development remain poorly defined. Using single-cell RNA and ATAC sequencing, we profile over 660,000 cells in the developing mouse hypothalamus and prethalamus between embryonic day 11 and postnatal day 8. This resource maps key transcriptional and chromatin dynamics underlying regionalization, neurogenesis, and neuronal subtype differentiation. We identify distinct neurogenic progenitor populations and uncover gene regulatory networks controlling their spatial and temporal identity. Integration with genome-wide association study data reveals that transcription factors active in supramammillary and prethalamic lineages are associated with metabolic and neuropsychiatric traits. Cross-repressive interactions among regional transcription factors reinforce hypothalamic boundaries. Functional analysis of Dlx1/2 shows that their loss disrupts GABAergic neuron specification, leading to impaired thalamic inhibition and hyperactivity. This study provides a foundational atlas of hypothalamic and prethalamic development and highlights the importance of early gene regulatory programs in health and disease.
    Keywords:  CP: Developmental biology; CP: Neuroscience; Dlx1; Dlx2; autism spectrum disorder; diencephalon; gene regulatory networks; hypothalamus; neurogenesis; prethalamus; single-cell multiomics; temporal patterning; thalamic reticular nucleus; zona incerta
    DOI:  https://doi.org/10.1016/j.celrep.2025.115858
  22. Commun Biol. 2025 Jun 11. 8(1): 908
    Spatial organization, chromatin accessibility and gene-regulatory programs defining mouse sensory neurons.
    Doris Krauter, Jussi Kupari, Dmitry Usoskin, Jie Su, Yizhou Hu, Ming-Dong Zhang, Patrik Ernfors.
      Heterogeneity among somatosensory neurons is necessary for internal and external sensation. Precise patterns of gene transcription orchestrated through enhancer activation maintain heterogeneity. Thus, high-resolution cell type classification, chromatin accessibility and its relation to enhancer activation can explain the governing principles for sensory neuron heterogeneity. Here, we present an integrated atlas from published high-quality scRNA-seq datasets and resequencing the dorsal root ganglion, including over 44,000 neurons. MERSCOPE spatial transcriptomics confirms cell types in situ, including previously unrecognized neuronal types, and a spatial zonation of both neurons and non-neuronal cells. We present a cell type specific open chromatin atlas revealing enhancer driven regulons and gene-regulatory networks organized into co-regulated gene-programs that together define sensory neuron diversity. Cell type complexity is shown to be generated by layered co-regulated transcriptional modules representing shared functions across different scales of the neuronal type hierarchy with cell type specific contribution as the exception.
    DOI:  https://doi.org/10.1038/s42003-025-08315-1
  23. Proc Natl Acad Sci U S A. 2025 Jun 17. 122(24): e2506321122
    Ligand-specific regulation of a binary enhancer code dictating cellular senescence.
    Thomas Suter, Meyer J Friedman, Cagdas Tazearslan, Daria Merkurjev, Kenny Ohgi, Dario Meluzzi, Michael G Rosenfeld, Yousin Suh.
      Cellular senescence, a major contributor to aging and age-related pathologies, is characterized by irreversible proliferative arrest and a disease-linked, proinflammatory profile known as the Senescence Associated Secretory Phenotype (SASP). A critical unanswered question is whether these properties are regulated by specific enhancer subsets, potentially licensing strategies that selectively block deleterious SASP components. Here, we identify two functionally distinct and independently regulated enhancer programs underlying senescence that are controlled by different TGF-β family ligands. Whereas Activin A stimulates recruitment of nuclear factor IA/C (NFIA/C) and SMAD2/3 transcription factors to an enhancer network that induces proliferation arrest, TGF-β2 promotes SMAD2/3-mediated suppression of a p65-dependent enhancer cohort driving the SASP. We have also uncovered reciprocal SMAD2/3-super-enhancer-regulated feedback loops that govern expression of the TGF-β2 (TGFB2) and Activin A (INHBA) transcription units, both of which are significantly up-regulated in replicative senescence. The characteristic enhancer usage and transcriptional landscape of high-passage senescent cells are sensitive to rapamycin treatment, discontinuation of which results in robust but selective senescent enhancer activation and exacerbation of the SASP. Collectively, this study uncovers separable enhancer programs and their key constituent transcription factors that contribute to the canonical features of cellular senescence, potentially informing the development of SASP-targeted therapies.
    Keywords:  NFI; SMAD2/3; cellular senescence; enhancers; p65
    DOI:  https://doi.org/10.1073/pnas.2506321122
  24. Nucleic Acids Res. 2025 Jun 06. pii: gkaf505. [Epub ahead of print]53(11):
    Super-enhancer-mediated circRNAs exhibit high splicing circularization diversity and transcriptional activity.
    Shaodong Huang, Yulong Han, Yiran Liu, Lina Bu, Chenyang Wu, Ziyan Rao, Chuan Ye, Hansen Cheng, Yunxi Liao, Yunan Sun, Yushu Zou, Zixu Wang, Bryan-Yu Sun, Shu Meng, Dongyu Zhao.
      Circular RNAs (circRNAs), an emerging subclass of noncoding RNAs, have been increasingly recognized as critical regulators in diverse biological functions and cellular processes. Despite their functional significance, the epigenetic mechanisms governing circRNA biogenesis remain poorly understood. Our study reveals that H3K27ac-marked super-enhancers (SEs) significantly enhance both circRNA splicing circularization diversity and transcriptional activation of their host genes. Intriguingly, other histone modifications-including H3K4me3, H3K36me3, H3K27me3, and H3K9me3-exhibit distinct regulatory effects on circRNA transcriptional activity. Through comprehensive analysis of 195 transcriptomic profiles, we identified a pan-cancer epigenomic tumor-suppressor signature termed CircRNA Isoform Reduction for Shortened Enhancers in cancer (CIRSE). Notably, CIRSE demonstrates strong prognostic potential in lung adenocarcinoma, as validated by comprehensive survival analyses. Combining Nanopore sequencing with CLIP-Seq approaches, we further elucidated the dual regulatory mechanism involving circRNA stability maintenance and back-splicing junction selection mediated by specific RNA-binding proteins. Functional validation confirmed that CIRSE-defined tumor-suppressive circRNAs are essential for maintaining malignant phenotypes in cancer models. Our findings not only provide mechanistic insights into the epigenetic regulation of circRNAs, but also pave the way for mutation-agnostic discovery of tumor-suppressive circRNAs in precision oncology applications.
    DOI:  https://doi.org/10.1093/nar/gkaf505
  25. Genome Biol. 2025 Jun 11. 26(1): 162
    MINGLE: a mutual information-based interpretable framework for automatic cell type annotation in single-cell chromatin accessibility data.
    Siyu Li, Yifan Huang, Shengquan Chen.
      Single-cell chromatin accessibility sequencing (scCAS) has proven invaluable for investigating the intricate landscape of epigenomic heterogeneity. We propose MINGLE, a mutual information-based interpretable framework that leverages cellular similarities and topological structures for accurate cell type annotation of scCAS data. Additionally, we introduce a convex hull-based strategy to effectively identify novel cell types. Extensive experiments demonstrate MINGLE's superior annotation performance, particularly for rare and novel cell types, delivering valuable biological insights compared to existing methods. Moreover, MINGLE excels in cross-batch, cross-tissue, and cross-species scenarios, showing robustness to data imbalance and size, highlighting its versatility for complex annotation tasks.
    DOI:  https://doi.org/10.1186/s13059-025-03603-9
  26. Cell Rep. 2025 Jun 05. pii: S2211-1247(25)00567-4. [Epub ahead of print]44(6): 115796
    Combinatorial transcriptional regulation establishes subtype-appropriate synaptic properties in auditory neurons.
    Isle Bastille, Lucy Lee, Cynthia Moncada-Reid, Wei-Ming Yu, Austen Sitko, Andrea Yung, Mina Zamani, Nele Christophersen, Reza Maroofian, Hamid Galehdari, Norbert Babai, Barbara Vona, Tobias Moser, Lisa Goodrich.
      Neurons develop diverse synapses that vary in content, morphology, and size. Although transcriptional regulators of neurotransmitter identity are known, it remains unclear how synaptic features are patterned among neuronal subtypes. In the auditory system, glutamatergic synaptic properties vary across three spiral ganglion neuron (SGN) subtypes that collectively encode sound. Here, we demonstrate that Maf transcription factors combinatorially shape synaptic properties in SGNs. SGN subtypes express different ratios of c-Maf and Mafb, which act redundantly to impart subtype identities and individually to shape subtype-appropriate gene expression programs. On their own, c-Maf and Mafb have independent and opposing effects on synaptic features and hearing. A mutation in the MAFB leucine zipper domain causes deafness in humans, underscoring the importance of regulated Maf activity for hearing. Thus, functional diversity and coordinated action of Maf family members enable flexible and robust control of gene expression needed to generate synaptic heterogeneity across neuronal subtypes.
    Keywords:  CP: Neuroscience; Maf transcription factors; autosomal recessive non-syndromic hearing loss; combinatorial codes; hearing; neuronal subtypes; spiral ganglion neurons; synaptic diversity
    DOI:  https://doi.org/10.1016/j.celrep.2025.115796
  27. Mol Cell. 2025 Jun 04. pii: S1097-2765(25)00459-9. [Epub ahead of print]
    Vostok: A looping factor for the organization of the regulatory genome in the Drosophila brain.
    Jie Hu, Xiao Li, Dmitry Lomaev, Nadezhda E Vorobyeva, Michael Levine, Maksim Erokhin, Darya Chetverina.
      Drosophila tethering elements mediate long-range enhancer-promoter interactions and connect the promoters of distant paralogous genes. Micro-C maps identified 645 such loops in the Drosophila larval brain, spanning distances of 25 to 250 kb. Here, we demonstrate that the MADF-containing Vostok protein acts as a looping factor. It binds to GCAACA motifs that are overrepresented in brain tethering elements. There is a loss of 47 (7%) of the loops in Vostok mutants, resulting in diminished expression of associated genes. Vostok is largely independent of another looping factor, GAGA-associated factor (GAF). Only 9 loops are disrupted in both Vostok and GAF mutants, raising the possibility of a combinatorial code for tether-tether interactions. This is supported by the reliance of two previously identified meta-loops spanning 6 Mb on both GAF and Vostok. We discuss the prospects of using different combinations of looping factors to engineer 3D associations in animal genomes.
    Keywords:  GAF, genome organization; TAD; Vostok, CG11504; looping factor; tethering elements
    DOI:  https://doi.org/10.1016/j.molcel.2025.05.020
This page is being maintained by Thomas Krichel. It was last updated on 2025‒06‒16 at 15:53.