bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2025–05–18
twenty-six papers selected by
Connor Rogerson, University of Cambridge
  1. High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion.
  2. Transcription factor cooperativity at a GATA3 tandem DNA sequence determines oncogenic enhancer-mediated activation.
  3. Deciphering the role of RNA in regulating CTCF's DNA binding affinity in leukemia cells.
  4. CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation.
  5. Temporally discordant chromatin accessibility and DNA demethylation define short- and long-term enhancer regulation during cell fate specification.
  6. Hierarchy in regulator interactions with distant transcriptional activation domains empowers rheostatic regulation.
  7. Three-dimensional genome landscape of primary human cancers.
  8. H2A.Z deposition by the SWR complex is stimulated by polyadenine DNA sequences in nucleosomes.
  9. Single amino acid mutations in histone H3.3 illuminate the functional significance of H3K4 methylation in plants.
  10. The regulatory potential of transposable elements in maize.
  11. Dual DNA demethylation mechanisms implement epigenetic memory driven by the pioneer factor PAX7.
  12. GATA3 differentially regulates the transcriptome via zinc finger 2-modulated phase separation.
  13. PNUTS:PP1 recruitment to Tox4 regulates chromosomal dispersal in Drosophila germline development.
  14. Transcription factors form a ternary complex with NIPBL/MAU2 to localize cohesin at enhancers.
  15. Multiomics Reveal Associations Between CpG Methylation, Histone Modifications and Transcription in a Species That has Lost DNMT3, the Colorado Potato Beetle.
  16. A specialized TFIIB is required for transcription of transposon-targeting noncoding RNAs.
  17. C/EBPα activates Irf8 expression in myeloid progenitors at the +56-kb enhancer to initiate cDC1 development.
  18. NRF2 supports non-small cell lung cancer growth independently of CBP/p300-enhanced glutathione synthesis.
  19. SMARCA4 loss increases RNA Polymerase II pausing and elevates R-loops to inhibit BRCA1-mediated repair in ovarian cancer.
  20. Image2Reg: Linking chromatin images to gene regulation using genetic and chemical perturbation screens.
  21. Identifying the DNA methylation preference of transcription factors using ProtBERT and SVM.
  22. Targeting transcription factors through an IMiD independent zinc finger domain.
  23. UTX (KDM6A) promotes differentiation noncatalytically in somatic self-renewing epithelia.
  24. PRMT3 reverses HIV-1 latency by increasing chromatin accessibility to form a TEAD4-P-TEFb-containing transcriptional hub.
  25. Mapping the Simultaneously Accessible and ssDNA-Containing Genome With KAS-ATAC Sequencing.
  26. Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticity.
  1. Nat Commun. 2025 May 15. 16(1): 4506
    High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion.
    Corriene E Sept, Y Esther Tak, Viraat Goel, Mital S Bhakta, Christian G Cerda-Smith, Haley M Hutchinson, Marco Blanchette, Christine E Eyler, Sarah E Johnstone, J Keith Joung, Anders S Hansen, Martin J Aryee.
      Cohesin-mediated DNA loop extrusion enables gene regulation by distal enhancers through the establishment of chromosome structure and long-range enhancer-promoter interactions. The best characterized cohesin-related structures, such as topologically associating domains (TADs) anchored at convergent CTCF binding sites, represent static conformations. Consequently, loop extrusion dynamics remain poorly understood. To better characterize static and dynamically extruding chromatin loop structures, we use MNase-based 3D genome assays to simultaneously determine CTCF and cohesin localization as well as the 3D contacts they mediate. Here we present CTCF Analyzer (with) Multinomial Estimation (CAMEL), a tool that identifies CTCF footprints at near base-pair resolution in CTCF MNase HiChiP. We also use Region Capture Micro-C to identify a CTCF-adjacent footprint that is attributed to cohesin occupancy. We leverage this substantial advance in resolution to determine that the fully extruded (CTCF-CTCF loop) state is rare genome-wide with locus-specific variation from ~1-10%. We further investigate the impact of chromatin state on loop extrusion dynamics and find that active regulatory elements impede cohesin extrusion. These findings support a model of topological regulation whereby the transient, partially extruded state facilitates enhancer-promoter contacts that can regulate transcription.
    DOI:  https://doi.org/10.1038/s41467-025-57775-w
  2. Cell Rep. 2025 May 14. pii: S2211-1247(25)00476-0. [Epub ahead of print]44(5): 115705
    Transcription factor cooperativity at a GATA3 tandem DNA sequence determines oncogenic enhancer-mediated activation.
    Joana R Costa, Yang Li, Nurkaiyisah Zaal Anuar, David O'Connor, Sunniyat Rahman, Tanya Rapoz-D'Silva, Kent T M Fung, Rachael Pocock, Zhaodong Li, Stephen Henderson, Lingyi Wang, Mateja E Krulik, Sara Hyseni, Nivedita Singh, George Morrow, Yanping Guo, Daisy O F Gresham, Javier Herrero, Richard G Jenner, A Thomas Look, Dennis Kappei, Marc R Mansour.
      The TAL1 oncogene driving T cell lymphoblastic leukemia is frequently activated through mutated cis-regulatory elements, whereby small insertions or deletions (indels) create a binding site for the transcription factor MYB. Unraveling how non-coding mutations create oncogenic enhancers is key to understanding cancer biology and can provide important insights into fundamental mechanisms of gene regulation. Utilizing a CRISPR-Cas9 screening approach, we identify GATA3 as the key transcriptional regulator of enhancer-mediated TAL1 overexpression. CRISPR-Cas9 engineering of the mutant enhancer reveals a tandem GATA3 site that is required for binding of GATA3, chromatin accessibility, and MYB recruitment. Reciprocally, MYB binding to its motif is required for GATA3 recruitment, consistent with a transcription factor cooperativity model. Importantly, we show that GATA3 stabilizes a TAL1-MYB interaction and that complex formation requires GATA3 binding to DNA. Our work sheds light on the mechanisms of enhancer-mediated oncogene activation, where key transcription factors cooperate to achieve maximal transcriptional output, thereby supporting leukemogenesis.
    Keywords:  CP: Cancer; CP: Molecular biology; DNA binding domain; GATA3; MYB; T cell acute lymphoblastic leukemia; T-ALL; TAL1; cooperativity; enhancer; motif; oncogene; transcription factor
    DOI:  https://doi.org/10.1016/j.celrep.2025.115705
  3. Genome Biol. 2025 May 12. 26(1): 126
    Deciphering the role of RNA in regulating CTCF's DNA binding affinity in leukemia cells.
    Judith Hyle, Wenjie Qi, Mohamed Nadhir Djekidel, Wojciech Rosikiewicz, Beisi Xu, Chunliang Li.
       BACKGROUND: CTCF, a highly studied transcription factor, is essential for chromatin interaction maintenance. Several independent studies report that CTCF interacts with RNAs in vitro and in cells. Yet continuous debates about the authenticity of the RNA-binding affinity of CTCF and its biological role remain in large part due to limited research techniques available, such as CLIP-seq.
    RESULT: Here, we investigate RNA's role in CTCF's transcription factor function through its chromatin occupancy. To systematically explore whether RNAs affect CTCF's ability to bind DNA, we perturb CTCF-RNA interactions by three independent approaches and examine CTCF genome occupancy by ChIP-seq. Although RNase A and triptolide treatment each affect a certain number of CTCF-binding peaks, few peaks overlap between treatment groups indicating the effect of RNA in regulating CTCF's DNA binding affinity is variable between loci. In addition, limited transcriptional or chromatin accessibility changes occur between cells expressing wild-type CTCF or CTCF lacking the RNA binding region.
    CONCLUSION: Our data provide a complementary approach and in silico evidence to consider the significance of RNA affecting CTCF's DNA binding affinity globally.
    Keywords:  Auxin-inducible degron; CTCF; Chromatin accessibility; RNA; Transcription
    DOI:  https://doi.org/10.1186/s13059-025-03582-x
  4. Nat Struct Mol Biol. 2025 May 13.
    CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation.
    Magdalena A Karpinska, Yi Zhu, Zahra Fakhraei Ghazvini, Shyam Ramasamy, Mariano Barbieri, T B Ngoc Cao, Natalie Varahram, Abrar Aljahani, Michael Lidschreiber, Argyris Papantonis, A Marieke Oudelaar.
      Enhancers and promoters interact in three-dimensional (3D) chromatin structures to regulate gene expression. Here we characterize the mechanisms that drive the formation and function of these structures in a lymphoid-to-myeloid transdifferentiation system. Based on analyses at base pair resolution, we demonstrate a close correlation between binding of regulatory proteins, formation of chromatin interactions and gene expression. Multi-way interaction analyses and computational modeling show that tissue-specific gene loci are organized into chromatin hubs, characterized by cooperative interactions between multiple enhancers, promoters and CTCF-binding sites. While depletion of CTCF strongly impairs the formation of these chromatin hubs, the effects of CTCF depletion on gene expression are modest and can be explained by rewired enhancer-promoter interactions. These findings demonstrate a role for enhancer-promoter interactions in gene regulation that is independent of cooperative interactions in chromatin hubs. Together, these results contribute to our understanding of the structure-function relationship of the genome during cellular differentiation.
    DOI:  https://doi.org/10.1038/s41594-025-01555-z
  5. Cell Rep. 2025 May 09. pii: S2211-1247(25)00451-6. [Epub ahead of print]44(5): 115680
    Temporally discordant chromatin accessibility and DNA demethylation define short- and long-term enhancer regulation during cell fate specification.
    Lindsey N Guerin, Timothy J Scott, Jacqueline A Yap, Annelie Johansson, Fabio Puddu, Tom Charlesworth, Yilin Yang, Alan J Simmons, Ken S Lau, Rebecca A Ihrie, Emily Hodges.
      Chromatin and DNA modifications mediate the transcriptional activity of lineage-specifying enhancers, but recent work challenges the dogma that joint chromatin accessibility and DNA demethylation are prerequisites for transcription. To understand this paradox, we established a highly resolved timeline of their dynamics during neural progenitor cell differentiation. We discovered that, while complete demethylation appears delayed relative to shorter-lived chromatin changes for thousands of enhancers, DNA demethylation actually initiates with 5-hydroxymethylation before appreciable accessibility and transcription factor occupancy is observed. The extended timeline of DNA demethylation creates temporal discordance appearing as heterogeneity in enhancer regulatory states. Few regions ever gain methylation, and resulting enhancer hypomethylation persists long after chromatin activities have dissipated. We demonstrate that the temporal methylation status of CpGs (mC/hmC/C) predicts past, present, and future chromatin accessibility using machine learning models. Thus, chromatin and DNA methylation collaborate on different timescales to shape short- and long-term enhancer regulation during cell fate specification.
    Keywords:  5-hydroxymethylation; 6-base sequencing; ATAC-Me; CP: Developmental biology; CP: Molecular biology; DNA methylation; chromatin accessibility; differentiation; enhancers; epigenetics; machine learning; neural progenitor cells
    DOI:  https://doi.org/10.1016/j.celrep.2025.115680
  6. Protein Sci. 2025 Jun;34(6): e70142
    Hierarchy in regulator interactions with distant transcriptional activation domains empowers rheostatic regulation.
    Amanda D Due, Norman E Davey, F Emil Thomasen, Nicholas Morffy, Andreas Prestel, Inna Brakti, Charlotte O'Shea, Lucia C Strader, Kresten Lindorff-Larsen, Karen Skriver, Birthe B Kragelund.
      Transcription factors carry long intrinsically disordered regions often containing multiple activation domains. Despite numerous recent high-throughput identifications and characterizations of activation domains, the interplay between sequence motifs, activation domains, and regulator binding in intrinsically disordered transcription factor regions remains unresolved. Here, we map sequence motifs and activation domains in an Arabidopsis thaliana NAC transcription factor clade, revealing that although sequence motifs and activation domains often coincide, no systematic overlap exists. Biophysical analyses using NMR spectroscopy show that the long intrinsically disordered region of senescence-associated transcription factor ANAC046 is devoid of residual structure. We identify two activation domain/sequence motif regions, one at each end that both bind a panel of six positive and negative regulator domains from biologically relevant regulators promiscuously. Binding affinities measured using isothermal titration calorimetry reveal a hierarchy for regulator binding of the two ANAC046 activation domain/sequence motif regions defining these as regulatory hotspots. Despite extensive dynamic intramolecular contacts along the disordered chain revealed using paramagnetic relaxation enhancement experiments and simulations, the regions remain uncoupled in binding. Together, the results imply rheostatic regulation by ANAC046 through concentration-dependent regulator competition, a mechanism likely mirrored in other transcription factors with distantly located activation domains.
    Keywords:  activation domains; intrinsically disordered region; isothermal titration calorimetry; nuclear magnetic resonance; protein–protein interactions; short linear motif; transcription factor
    DOI:  https://doi.org/10.1002/pro.70142
  7. Nat Genet. 2025 May;57(5): 1189-1200
    Three-dimensional genome landscape of primary human cancers.
    Cancer Genome Atlas Analysis Network
      Genome conformation underlies transcriptional regulation by distal enhancers, and genomic rearrangements in cancer can alter critical regulatory interactions. Here we profiled the three-dimensional genome architecture and enhancer connectome of 69 tumor samples spanning 15 primary human cancer types from The Cancer Genome Atlas. We discovered the following three archetypes of enhancer usage for over 100 oncogenes across human cancers: static, selective gain or dynamic rewiring. Integrative analyses revealed the enhancer landscape of noncancer cells in the tumor microenvironment for genes related to immune escape. Deep whole-genome sequencing and enhancer connectome mapping provided accurate detection and validation of diverse structural variants across cancer genomes and revealed distinct enhancer rewiring consequences from noncoding point mutations, genomic inversions, translocations and focal amplifications. Extrachromosomal DNA promoted more extensive enhancer rewiring among several types of focal amplification mechanisms. These results suggest a systematic approach to understanding genome topology in cancer etiology and therapy.
    DOI:  https://doi.org/10.1038/s41588-025-02188-0
  8. PLoS Biol. 2025 May;23(5): e3003059
    H2A.Z deposition by the SWR complex is stimulated by polyadenine DNA sequences in nucleosomes.
    Cynthia Converso, Leonidas Pierrakeas, Lirong Chan, Shalvi Chowdhury, Emily de Onis, Vyacheslav I Kuznetsov, John M Denu, Ed Luk.
      The variant histone H2A.Z is deposited into nucleosomes immediately downstream of promoters, where it plays a critical role in transcription. The site-specific deposition of H2A.Z is catalyzed by the SWR complex, a conserved chromatin remodeler with affinity for promoter-proximal nucleosome-depleted regions (NDRs) and histone acetylation. By comparing the genomic distribution of H2A.Z in wild-type and SWR-deficient cells, we found that SWR is also responsible for depositing H2A.Z at thousands of non-canonical sites not directly linked to NDRs or histone acetylation. To understand the targeting mechanism of H2A.Z, we presented SWR to a library of canonical nucleosomes isolated from yeast and analyzed the preferred substrates. Our results revealed that SWR preferentially deposited H2A.Z into a subset of endogenous H2A.Z sites, which are overrepresented by polyadenine tracts on the top strands of the DNA duplex at the nucleosomal entry-exit sites. Insertion of polyadenine sequences into recombinant nucleosomes near the outgoing H2A-H2B dimer enhanced SWR's affinity for the nucleosomal substrate and increased its H2A.Z insertion activity. These findings suggest that the genome encodes sequence-based information that facilitates remodeler-mediated targeting of H2A.Z.
    DOI:  https://doi.org/10.1371/journal.pbio.3003059
  9. Nat Commun. 2025 May 13. 16(1): 4408
    Single amino acid mutations in histone H3.3 illuminate the functional significance of H3K4 methylation in plants.
    Mande Xue, Lijun Ma, Xiaoyi Li, Huairen Zhang, Fengyue Zhao, Qian Liu, Danhua Jiang.
      Although histone modifications are linked with chromatin activities such as transcription, proofs of their causal importance remain limited. Sequence variants within each histone family expand chromatin diversity and may carry specific modifications, further raising questions about their coordination. Here, we investigate the role of lysine 4 (K4) in two Arabidopsis H3 variants, H3.1 and H3.3. K4 is essential for H3.3 function but not H3.1 in plant development. Mutating K4 in H3.3 drastically reduced H3K4 methylation levels and mimicked the transcriptomic effects of losing SDG2, the major H3K4 trimethylation (H3K4me3) methyltransferase. Moreover, H3.3K4 and SDG2 are required for de novo gene activation and RNA Pol II elongation. H3K4 methylation is preferentially enriched on H3.3, likely due to the coordinated activity of H3.3 deposition and H3K4 methylation. Furthermore, we reveal the diverse impacts of K4 nearby residue mutations on H3K4 methylation and H3.3 function. These findings highlight H3.3 as a critical substrate for H3K4 methylation, which is important for gene expression regulation.
    DOI:  https://doi.org/10.1038/s41467-025-59711-4
  10. Nat Plants. 2025 May 13.
    The regulatory potential of transposable elements in maize.
    Kerry L Bubb, Morgan O Hamm, Thomas W Tullius, Joseph K Min, Bryan Ramirez-Corona, Nicholas A Mueth, Jane Ranchalis, Yizi Mao, Erik J Bergstrom, Mitchell R Vollger, Cole Trapnell, Josh T Cuperus, Andrew B Stergachis, Christine Queitsch.
      The genomes of flowering plants consist largely of transposable elements (TEs), some of which modulate gene regulation and function. However, the repetitive nature of TEs and difficulty of mapping individual TEs by short-read sequencing have hindered our understanding of their regulatory potential. Here we show that long-read chromatin fibre sequencing (Fiber-seq) comprehensively identifies accessible chromatin regions (ACRs) and CpG methylation across the maize genome. We uncover stereotypical ACR patterns at young TEs that degenerate with evolutionary age, resulting in TE enhancers preferentially marked by a novel plant-specific epigenetic feature: simultaneous hyper-CpG methylation and chromatin accessibility. We show that TE ACRs are co-opted as gene promoters and that ACR-containing TEs can facilitate gene amplification. Lastly, we uncover a pervasive epigenetic signature-hypo-5mCpG methylation and diffuse chromatin accessibility-directing TEs to specific loci, including the loci that sparked McClintock's discovery of TEs.
    DOI:  https://doi.org/10.1038/s41477-025-02002-z
  11. Sci Adv. 2025 May 16. 11(20): eadu6632
    Dual DNA demethylation mechanisms implement epigenetic memory driven by the pioneer factor PAX7.
    Juliette Harris, Alexandre Mayran, Arthur Gouhier, Yves Gauthier, Nawal Hajj Sleiman, Samir Merabet, Michael Dukatz, Pavel Bashtrykov, Albert Jeltsch, Haig Djambazian, Shu-Huang Chen, Aurelio Balsalobre, Jacques Drouin.
      Pioneer transcription factors have the unique ability to open chromatin at enhancers to implement new cell fates. They also provide epigenetic memory through demethylation of enhancer DNA, but the underlying mechanisms remain unclear. We now show that the pioneer paired box 7 (PAX7) triggers DNA demethylation using two replication-dependent mechanisms, including direct PAX7 interaction with the E3 ubiquitin-protein ligase (UHRF1)-DNA methyltransferase 1 (DNMT1) complex that is responsible for DNA methylation maintenance. PAX7 binds to UHRF1 and prevents its interaction with DNMT1, thus blocking activation of its enzyme activity. The ten-eleven translocation DNA dioxygenase (TET) DNA demethylases also contribute to the replication-dependent loss of DNA methylation. Thus, PAX7 hijacks UHRF1 to block activation of DNMT1 after replication, leading to loss of DNA methylation by dilution, and the process is assisted by the action of TET demethylases.
    DOI:  https://doi.org/10.1126/sciadv.adu6632
  12. Cell Rep. 2025 May 14. pii: S2211-1247(25)00473-5. [Epub ahead of print]44(5): 115702
    GATA3 differentially regulates the transcriptome via zinc finger 2-modulated phase separation.
    Yatao Chen, Yajie Wan, Xiaoying Pei, Ziqi Wei, Tan Wang, Jun Zhang, Liming Chen.
      Phase separation (PS) underlies gene control by transcription factors. However, little is known about whether and how DNA-binding domains (DBDs) regulate the PS for transcription factors to differentially regulate the transcriptome. The transcription factor GATA3, a master immune regulator, is frequently mutated in breast cancer. Here, we report that GATA3 undergoes DBD-modulated PS to mediate the formation of chromatin condensates. We show that the DBD regulates the GATA3 PS through its zinc finger 2 (ZnF2) domain, which provides positive charges for multivalent electrostatic interactions mainly via two arginine amino acids, R329 and R330. Compared with breast-cancer-associated GATA3 without ZnF2-defective mutations, breast cancer GATA3 with ZnF2-defective mutations causes aberrant ZnF2-modulated PS and condensate formation to remodel the differentially regulated transcriptome, resulting in a favorable prognosis for patients and reduced tumor growth in mice. Therefore, GATA3 demonstrates a principle of how a transcription factor differentially regulates the transcriptome via DBD-modulated PS.
    Keywords:  CP: Molecular biology; DNA-binding domain; GATA3; breast cancer; differentially regulated transcriptome; estrogen alpha-related gene expression; immune-related gene expression; phase separation; transcription factor; zinc finger
    DOI:  https://doi.org/10.1016/j.celrep.2025.115702
  13. Cell Rep. 2025 May 09. pii: S2211-1247(25)00464-4. [Epub ahead of print]44(5): 115693
    PNUTS:PP1 recruitment to Tox4 regulates chromosomal dispersal in Drosophila germline development.
    Louise Duncalf, Xinru Wang, Abdulrahman A Aljabri, Amy E Campbell, Rawan Q Alharbi, Ian Donaldson, Andrew Hayes, Wolfgang Peti, Rebecca Page, Daimark Bennett.
      Ser/Thr protein phosphatase 1 (PP1) forms a large nuclear holoenzyme (with PNUTS, WDR82, and Tox4) whose emerging role is to regulate transcription. However, the role of Tox4, and its interplay with the other phosphatase subunits in this complex, is poorly understood. Here, we combine biochemical, structural, cellular, and in vivo experiments to show that, while tox4 is dispensable for viability, it is essential for fertility, having both PNUTS-dependent and -independent roles in Drosophila germline development. We also show that Tox4 requires zinc for PNUTS TFIIS N-terminal domain (TND) binding, and that it binds the TND on a surface distinct from that used by established TND-interacting transcriptional regulators. We also show that selective disruption of the PNUTS-Tox4 and the PNUTS-PP1 interaction is critical for normal gene expression and chromosomal dispersal during oogenesis. Together, these data demonstrate how interactions within the PNUTS-Tox4-PP1 phosphatase combine to tune transcriptional outputs driving developmental transitions.
    Keywords:  CP: Developmental biology; CP: Molecular biology; Drosophila; PNUTS; PPP1R10; PTW/PP1 complex; Tox4; germline development; protein phosphatase 1; transcription
    DOI:  https://doi.org/10.1016/j.celrep.2025.115693
  14. Nucleic Acids Res. 2025 May 10. pii: gkaf415. [Epub ahead of print]53(9):
    Transcription factors form a ternary complex with NIPBL/MAU2 to localize cohesin at enhancers.
    Gregory Fettweis, Kaustubh Wagh, Diana A Stavreva, Alba Jiménez-Panizo, Sohyoung Kim, Michelle Lion, Andrea Alegre-Martí, Lorenzo Rinaldi, Thomas A Johnson, Elise Gilson, Manan Krishnamurthy, Li Wang, David A Ball, Tatiana S Karpova, Arpita Upadhyaya, Didier Vertommen, Juan Fernández Recio, Eva Estébanez-Perpiñá, Franck Dequiedt, Gordon L Hager.
      While the cohesin complex is a key player in genome architecture, how it localizes to specific chromatin sites is not understood. Recently, we and others have proposed that direct interactions with transcription factors lead to the localization of the cohesin-loader complex (NIPBL/MAU2) within enhancers. Here, we identify two clusters of LxxLL motifs within the NIPBL sequence that regulate NIPBL dynamics, interactome, and NIPBL-dependent transcriptional programs. One of these clusters interacts with MAU2 and is necessary for the maintenance of the NIPBL-MAU2 heterodimer. The second cluster binds specifically to the ligand-binding domains of steroid receptors. For the glucocorticoid receptor (GR), we examine in detail its interaction surfaces with NIPBL and MAU2. Using AlphaFold2 and molecular docking algorithms, we uncover a GR-NIPBL-MAU2 ternary complex and describe its importance in GR-dependent gene regulation. Finally, we show that multiple transcription factors interact with NIPBL-MAU2, likely using interfaces other than those characterized for GR.
    DOI:  https://doi.org/10.1093/nar/gkaf415
  15. J Exp Zool B Mol Dev Evol. 2025 May 12.
    Multiomics Reveal Associations Between CpG Methylation, Histone Modifications and Transcription in a Species That has Lost DNMT3, the Colorado Potato Beetle.
    Zoe M Länger, Elisa Israel, Jan Engelhardt, Agata I Kalita, Claudia I Keller Valsecchi, Joachim Kurtz, Sonja J Prohaska.
      Insects display exceptional phenotypic plasticity, which can be mediated by epigenetic modifications, including CpG methylation and histone modifications. In vertebrates, both are interlinked and CpG methylation is associated with gene repression. However, little is known about these regulatory systems in invertebrates, where CpG methylation is mainly restricted to gene bodies of transcriptionally active genes. A widely conserved mechanism involves the co-transcriptional deposition of H3K36 trimethylation and the targeted methylation of unmethylated CpGs by the de novo DNA methyltransferase DNMT3. However, DNMT3 has been lost multiple times in invertebrate lineages raising the question of how the links between CpG methylation, histone modifications and gene expression are affected by its loss. Here, we report the epigenetic landscape of Leptinotarsa decemlineata, a beetle species that has lost DNMT3 but retained CpG methylation. We combine RNA-seq, enzymatic methyl-seq and CUT&Tag to study gene expression, CpG methylation and patterns of H3K36me3 and H3K27ac histone modifications on a genome-wide scale. Despite the loss of DNMT3, H3K36me3 mirrors CpG methylation patterns. Together, they give rise to signature profiles for expressed and not expressed genes. H3K27ac patterns show a prominent peak at the transcription start site that is predictive of expressed genes irrespective of their methylation status. Our study provides new insights into the evolutionary flexibility of epigenetic modification systems that urge caution when generalizing across species.
    Keywords:  CUT&Tag; Coleoptera; EM‐seq; H3K27ac; H3K36me3; RNA‐seq
    DOI:  https://doi.org/10.1002/jez.b.23303
  16. Nucleic Acids Res. 2025 May 10. pii: gkaf427. [Epub ahead of print]53(9):
    A specialized TFIIB is required for transcription of transposon-targeting noncoding RNAs.
    Xia Cai, Zhihao Zhai, Tomoko Noto, Gang Dong, Xue Wang, Mingmei Liucong, Yujie Liu, Christiane Agreiter, Josef Loidl, Kazufumi Mochizuki, Miao Tian.
      Transposable elements (TEs) pose threats to genome stability. Therefore, small RNA-mediated heterochromatinization suppresses the transcription and hence the mobility of TEs. Paradoxically, transcription of noncoding RNA (ncRNA) from TEs is needed for the production of TE-targeting small RNAs and/or recruiting the silencing machinery to TEs. Hence, specialized RNA polymerase II (Pol II) regulators are required for such unconventional transcription in different organisms, including the developmental stage-specific Mediator complex (Med)-associated proteins in the ncRNA transcription from TE-related sequences in Tetrahymena. Yet it remains unclear how the Pol II transcriptional machinery is assembled at TE-related sequences for the ncRNA transcription. Here, we report that Pol II is regulated by Emit3, a stage-specific TFIIB-like protein specialized in TE transcription. Emit3 interacts with the TFIIH complex and localizes to TE-dense regions, especially at sites enriched with a G-rich sequence motif. Deletion of Emit3 globally abolishes Pol II-chromatin association in the meiotic nucleus, disrupts the chromatin binding of Med, and impairs the TE-biased localization of TFIIH. Conversely, Emit3's preferential localization to TE-rich loci relies in part on Med-associated proteins. These findings suggest that Emit3, TFIIH, and Med-associated proteins work together to initiate Pol II ncRNA transcription from TE-dense regions, possibly in a sequence-dependent manner.
    DOI:  https://doi.org/10.1093/nar/gkaf427
  17. Sci Immunol. 2025 May 16. 10(107): eadt5899
    C/EBPα activates Irf8 expression in myeloid progenitors at the +56-kb enhancer to initiate cDC1 development.
    Jing Chen, Tian-Tian Liu, Feiya Ou, Ray A Ohara, Suin Jo, Joshua Luke Postoak, Takeshi Egawa, Ryan B Day, Theresa L Murphy, Kenneth M Murphy, Sunkyung Kim.
      Development of type 1 conventional dendritic cells (cDC1s) underlies the capacity to generate antiviral and antitumor immune responses. Here, we identify the basis for cDC1 development from its earliest progenitors, determining the hierarchy of several required transcription factors and uncovering a series of mandatory cis interactions between constituent enhancers within the Irf8 superenhancer. We produced in vivo mutations of two C/EBPα binding sites that comprise the Irf8 +56-kilobase (kb) enhancer that markedly reduced IRF8 expression in all myeloid progenitors and impaired cDC1 development. These sites did not bind RUNX1 or RUNX3, and C/EBPα expression was instead regulated by their action at the Cebpa +37-kb enhancer, placing RUNX factors upstream of Cebpa in regulating Irf8. Last, we demonstrate that cis interactions between the +56-kb Irf8 enhancer and the previously reported +41- and +32-kb Irf8 enhancers are mandatory in the sequential progression of these stage-specific constituent elements.
    DOI:  https://doi.org/10.1126/sciimmunol.adt5899
  18. EMBO Rep. 2025 May 14.
    NRF2 supports non-small cell lung cancer growth independently of CBP/p300-enhanced glutathione synthesis.
    Ryan J Conrad, James A Mondo, Mike Lingjue Wang, Peter S Liu, Zijuan Lai, Feroza K Choudhury, Qingling Li, Weng Ruh Wong, James Lee, Frances Shanahan, Eva Lin, Scott Martin, Joachim Rudolph, John G Moffat, Dewakar Sangaraju, Wendy Sandoval, Timothy Sterne-Weiler, Scott A Foster.
      Nuclear factor erythroid 2-related factor 2 (NRF2) is a stress responsive transcription factor that is mutationally activated in a subset (~25%) of clinically-aggressive non-small cell lung cancers (NSCLC). Mechanistic insight into drivers of the NRF2 dependency remains poorly understood. Here, we defined a novel NRF2 target gene set linked to NRF2-dependency in cancer cell lines, and observed that a significant portion of these genes is devoid of promoter-proximal NRF2 occupancy. Using integrated genomic analyses, we characterized extensive NRF2-dependent enhancer RNA (eRNA) synthesis and NRF2-mediated H3K27ac deposition at proximal and distal enhancer regions regulating these genes. While CBP/p300 is a well-validated direct interaction partner of NRF2 with prominent functions at enhancers, we report that this interaction is not required for NRF2-dependent NSCLC cell growth, indicating that NRF2 can sustain sufficient transcriptional activity in the absence of CBP/p300 coactivation. Broad metabolic profiling established a primary role for CBP/p300 in NRF2-dependent accumulation of glutathione and glutathione-related metabolites. While redox homeostasis via enhanced glutathione production is commonly associated with the normal physiological role of NRF2, collectively our results suggest that NRF2-dependent cancer cell growth does not require this enhanced glutathione production.
    Keywords:  CBP/p300; Glutathione; NRF2; Non-small Cell Lung Cancer; ROS
    DOI:  https://doi.org/10.1038/s44319-025-00463-z
  19. Cancer Res. 2025 May 14.
    SMARCA4 loss increases RNA Polymerase II pausing and elevates R-loops to inhibit BRCA1-mediated repair in ovarian cancer.
    Xianbing Zhu, Zheng Fu, Giulio Aceto, Jonathan St-Germain, Kexin Liu, Azadeh Arabzadeh, Yuxuan Qi, Yibo Xue, Leora Witkowski, Elise Graulich, Jutta Steinberger, Selim Misirlioglu, Nicklas Bassani, Racim Sansal, Amber Yasmeen, Geneviève Morin, Jingjie Guo, Anie Monast, Virginie Pilon, Alica Valachová, Kitty Pavlakis, Lili Fu, Walter H Gotlieb, W Glenn McCluggage, David Huntsman, Alexander J R Bishop, Douglas A Levine, Morag Park, Yemin Wang, Brian Raught, William D Foulkes, Sidong Huang.
      Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare, aggressive cancer affecting young women, driven by inactivating mutations in SMARCA4, a key SWI/SNF chromatin remodeling gene. To uncover its druggable vulnerabilities, we performed a compound screen and found that SCCOHT cells and tumors were sensitive to PARP inhibitors. Paradoxically, SCCOHT displayed BRCA-deficient traits despite retaining wild-type BRCA1 expression. Elevated R-loop in SCCOHT sequestered BRCA1, limiting its availability for DNA damage repair. Proximity-dependent biotin identification revealed that wild-type SMARCA4, but not its pathogenic variants, promoted RNA polymerase II (Pol II) elongation by mediating the assembly of the polymerase-associated factor 1 (PAF1) complex. Thus, SMARCA4 loss increased Pol II pausing, resulting in elevated R-loops and BRCA1 redistribution. The suppression of BRCA1 activity sensitized SMARCA4-deficient SCCOHT cells and tumors to PARP inhibitors, which was further enhanced by the addition of a CDK9 inhibitor targeting Pol II elongation. Co-targeting PARP/CDK9 also elicited synergistic effects against other undifferentiated ovarian cancer cells with SMARCA4 loss. These findings link SMARCA4 loss to perturbed Pol II elongation and compromised DNA repair by BRCA1, providing a therapeutic opportunity to target SCCOHT and other SWI/SNF-deficient ovarian cancers.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-24-3990
  20. Cell Syst. 2025 May 09. pii: S2405-4712(25)00126-7. [Epub ahead of print] 101293
    Image2Reg: Linking chromatin images to gene regulation using genetic and chemical perturbation screens.
    Daniel Paysan, Adityanarayanan Radhakrishnan, Xinyi Zhang, G V Shivashankar, Caroline Uhler.
      Representation learning provides an opportunity to uncover the link between 3D genome organization and gene regulatory networks, thereby connecting the physical and the biochemical space of a cell. Our method, Image2Reg, uses chromatin images obtained in large-scale genetic and chemical perturbation screens. Through convolutional neural networks, Image2Reg generates gene embedding that represents the effect of gene perturbation on chromatin organization. In addition, combining protein-protein interaction data with cell-type-specific transcriptomic data through a graph convolutional network, we obtain a gene embedding that represents the regulatory effect of genes. Finally, Image2Reg learns a map between the resulting physical and biochemical representation of cells, allowing us to predict the perturbed gene modules based on chromatin images. Our results confirm the deep link between chromatin organization and gene regulation and demonstrate that it can be harnessed to identify drug targets and genes upstream of perturbed phenotypes from a simple and inexpensive chromatin staining.
    Keywords:  chromatin; drug targets; gene regulation; genome organization; machine learning; microscopy imaging; multiomics; perturbations; representation learning
    DOI:  https://doi.org/10.1016/j.cels.2025.101293
  21. PLoS Comput Biol. 2025 May 13. 21(5): e1012513
    Identifying the DNA methylation preference of transcription factors using ProtBERT and SVM.
    Yanchao Li, Quan Zou, Qi Dai, Antony Stalin, Ximei Luo.
      Transcription factors (TFs) can affect gene expression by binding to certain specific DNA sequences. This binding process of TFs may be modulated by DNA methylation. A subset of TFs that serve as methylation readers preferentially binds to certain methylated DNA and is defined as TFPM. The identification of TFPMs enhances our understanding of DNA methylation's role in gene regulation. However, their experimental identification is resource-demanding. In this study, we propose a novel two-step computational approach to classify TFs and TFPMs. First, we employed a fine-tuned ProtBERT model to differentiate between the classes of TFs and non-TFs. Second, we combined the Reduced Amino Acid Category (RAAC) with K-mer and SVM to predict the potential of TFs to bind to methylated DNA. Comparative experiments demonstrate that our proposed methods outperform all existing approaches and emphasize the efficiency of our computational framework in classifying TFs and TFPMs. Cross-species validation on an independent mouse dataset further demonstrates the generalizability of our proposed framework In addition, we conducted predictions on all human transcription factors and found that most of the top 20 proteins belong to the Krueppel C2H2-type Zinc-finger family. So far, some studies have demonstrated a partial correlation between this family and DNA methylation and confirmed the preference of some of its members, thereby showing the robustness of our approach.
    DOI:  https://doi.org/10.1371/journal.pcbi.1012513
  22. EMBO Mol Med. 2025 May 14.
    Targeting transcription factors through an IMiD independent zinc finger domain.
    Bee Hui Liu, Miao Liu, Sridhar Radhakrishnan, Meng-Yuan Dai, Chaitanya Kumar Jaladanki, Chong Gao, Jing Ping Tang, Kalpana Kumari, Mei Lin Go, Kim Anh L Vu, Junsu Kwon, Hyuk-Soo Seo, Kijun Song, Xi Tian, Li Feng, Justin L Tan, Arek V Melkonian, Zhaoji Liu, Gerburg Wulf, Haribabu Arthanari, Jun Qi, Sirano Dhe-Paganon, John G Clohessy, Yeu Khai Choong, J Sivaraman, Hao Fan, Daniel G Tenen, Li Chai.
      Immunomodulatory imide drugs (IMiDs) degrade specific C2H2 zinc finger degrons in transcription factors, making them effective against certain cancers. SALL4, a cancer driver, contains seven C2H2 zinc fingers in three clusters, including an IMiD degron in zinc finger cluster one (ZFC1). Surprisingly, IMiDs do not inhibit the growth of SALL4-expressing cancer cells. To overcome this limit, we focused on a non-IMiD domain, SALL4 zinc finger cluster four (ZFC4). By combining ZFC4-DNA crystal structure and an in silico docking algorithm, in conjunction with cell viability assays, we screened several chemical libraries against a potentially druggable binding pocket, leading to the discovery of SH6, a compound that selectively targets SALL4-expressing cancer cells. Mechanistic studies revealed that SH6 degrades SALL4 protein through the CUL4A/CRBN pathway, while deletion of ZFC4 abolished this activity. Moreover, SH6 treatment led to a significant 87% tumor growth inhibition of SALL4+ patient-derived xenografts and demonstrated good bioavailability in pharmacokinetic studies. In summary, these studies represent a new approach for IMiD independent drug discovery targeting C2H2 transcription factors such as SALL4 in cancer.
    Keywords:  C2H2; Degrader; IMiD; SALL4; Zinc Finger Cluster Four (ZFC4)
    DOI:  https://doi.org/10.1038/s44321-025-00241-3
  23. Proc Natl Acad Sci U S A. 2025 May 20. 122(20): e2422971122
    UTX (KDM6A) promotes differentiation noncatalytically in somatic self-renewing epithelia.
    Gina N Pacella, Nina Kuprasertkul, Lydia Bao, Sijia Huang, Carina D'souza, Stephen M Prouty, Amy Anderson, Alexandra M Maldonado López, Morgan Sinkfield, Cyria Olingou, John T Seykora, Brian C Capell.
      The X-linked histone demethylase, UTX (KDM6A), is a master regulator of gene enhancers, though its role in self-renewing epithelia like the skin is not well understood. Here, we find that UTX is a key regulator of skin differentiation via the regulation of retinoic acid (RA) signaling, an essential metabolic pathway in both skin homeostasis, as well as in the treatment of an array of skin conditions ranging from cancer and acne to aging. Through deletion of Utx in the skin, we demonstrate direct regulation of both retinoid metabolic genes such as Crabp2, as well as key genes involved in epidermal stem cell fate and differentiation (i.e., Cdh1, Grhl3, Ctnnb1). Spatial analyses show that UTX loss dysregulates epidermal, sebaceous, and hair follicle differentiation programs. Strikingly, this only occurs in homozygous females, demonstrating that UTX's Y-linked paralog, UTY (Kdm6c), can compensate in males. Further, we observe genome-wide losses of H3K27 acetylation (H3K27ac) with minimal changes in H3K27 trimethylation (H3K27me3), revealing that UTX functions primarily noncatalytically to promote skin homeostasis. Together, the elucidation of these links between epigenetics, metabolic signaling, and epithelial differentiation offers new insights into how epigenetic modulation may allow for fine-tuning of key signaling pathways to treat disease.
    Keywords:  differentiation; epigenetics; retinoid signaling; sex bias; skin biology
    DOI:  https://doi.org/10.1073/pnas.2422971122
  24. Nat Commun. 2025 May 15. 16(1): 4529
    PRMT3 reverses HIV-1 latency by increasing chromatin accessibility to form a TEAD4-P-TEFb-containing transcriptional hub.
    Xinyu Wang, Yuhua Xue, Lin Li, Jinwen Song, Lei Jia, Xu Li, Miao Fan, Lu Lu, Wen Su, Jingwan Han, Dandan Lin, Rongdiao Liu, Xiang Gao, Yafei Guo, Zixun Xiang, Chunjing Chen, Linyu Wan, Huihui Chong, Yuxian He, Fusheng Wang, Kaihu Yao, Qiang Zhou, Dan Yu.
      Latent HIV-1 presents a formidable challenge for viral eradication. HIV-1 transcription and latency reversal require interactions between the viral promoter and host proteins. Here, we perform the dCas9-targeted locus-specific protein analysis and discover the interaction of human arginine methyltransferase 3 (PRMT3) with the HIV-1 promoter. This interaction reverses latency in cell line models and primary cells from latently infected persons by increasing the levels of H4R3Me2a and transcription factor P-TEFb at the viral promoter. PRMT3 is found to promote chromatin accessibility and transcription of HIV-1 and a small subset of host genes in regions harboring the classical recognition motif for another transcription factor TEAD4. This motif attracts TEAD4 and PRMT3 to the viral promoter to synergistically activate transcription. Physical interactions among PRMT3, P-TEFb, and TEAD4 exist, which may help form a transcriptional hub at the viral promoter. Our study reveals the potential of targeting these hub proteins to eradicate latent HIV-1.
    DOI:  https://doi.org/10.1038/s41467-025-59578-5
  25. Bio Protoc. 2025 May 05. 15(9): e5306
    Mapping the Simultaneously Accessible and ssDNA-Containing Genome With KAS-ATAC Sequencing.
    Georgi K Marinov, William J Greenleaf.
      The KAS-ATAC assay provides a method to capture genomic DNA fragments that are simultaneously physically accessible and contain single-stranded DNA (ssDNA) bubbles. These are characteristic features of two of the key processes involved in regulating and expressing genes-on one hand, the activity of cis-regulatory elements (cREs), which are typically devoid of nucleosomes when active and occupied by transcription factors, and on the other, the association of RNA polymerases with DNA, which results in the presence of ssDNA structures. Here, we present a detailed protocol for carrying out KAS-ATAC as well as basic processing of KAS-ATAC datasets and discuss the key considerations for its successful application. Key features • Allows mapping of simultaneously accessible and ssDNA-containing DNA fragments. • Describes the execution of N3-kethoxal labeling and transposition of native chromatin. • Describes the pulldown of biotin-labeled DNA fragments and library generation. • Describes basic KAS-ATAC data processing steps.
    Keywords:  ATAC-seq; Chromatin; Chromatin accessibility; KAS-ATAC; KAS-seq; Transcription; ssDNA
    DOI:  https://doi.org/10.21769/BioProtoc.5306
  26. Dev Cell. 2025 May 06. pii: S1534-5807(25)00251-5. [Epub ahead of print]
    Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticity.
    Yunyun Xu, Daohua Lou, Ping Chen, Gang Li, Dimtry Usoskin, Jian Pan, Fang Li, Shungen Huang, Caroline Hess, Ruze Tang, Xiaohan Hu, Juanjuan Yu, Maria Arceo, Ronald R de Krijger, Arthur S Tischler, Susanne Schlisio, Patrik Ernfors, Yizhou Hu, Jian Wang.
      Neuroblastoma, the most prevalent extracranial pediatric solid tumor, arises from neural crest progeny cells. It exhibits substantial developmental plasticity and intratumoral heterogeneity, leading to survival rates below 50% in high-risk cases. The regulatory mechanisms underlying this plasticity remain largely elusive. In this integrative study, we used single-cell MultiOmics from a mouse spontaneous tumor model and spatial transcriptomics from human patient samples to dissect the transcriptional and epigenetic landscapes that govern developmental states in neuroblastoma. We identified developmental intermediate states in high-risk neuroblastomas critical for malignant transitions and uncovered extensive epigenetic priming with latent capacity for diverse state transitions. Furthermore, we mapped enhancer gene regulatory networks (eGRNs) and tumor microenvironments sustaining these aggressive states. State transitions and malignancy could be interfered with by targeting transcription factors controlling the eGRNs.
    Keywords:  development; developmental plasticity; epigenetic priming; gene regulatory network; intermediate state; intratumoral heterogeneity; microenvironment; neuroblastoma; single-cell MultiOmics; spatial transcriptomics
    DOI:  https://doi.org/10.1016/j.devcel.2025.04.013
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