bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2025–03–09
sixteen papers selected by
Connor Rogerson, University of Cambridge
  1. CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis.
  2. Structure-function relationship of ASH1L and histone H3K36 and H3K4 methylation.
  3. Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome.
  4. Distinct gene regulatory dynamics drive skeletogenic cell fate convergence during vertebrate embryogenesis.
  5. PRC1 and PRC2 proximal interactome in mouse embryonic stem cells.
  6. Ubiquitous MEIS transcription factors actuate lineage-specific transcription to establish cell fate.
  7. ZBTB16/PLZF regulates juvenile spermatogonial stem cell development through an extensive transcription factor poising network.
  8. CODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to regulate the histone supply.
  9. Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage.
  10. Interplay between CTCF-binding and CTCF-lacking regulatory elements in generating an architectural stripe at the Igh locus.
  11. CTCF-mediated 3D chromatin sets up the gene expression program in the male germline.
  12. Increased levels of lagging strand polymerase α in an adult stem cell lineage affect replication-coupled histone incorporation.
  13. Capturing cell-type-specific activities of cis-regulatory elements from peak-based single-cell ATAC-seq.
  14. Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements.
  15. TFIIH kinase CDK7 drives cell proliferation through a common core transcription factor network.
  16. Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.
  1. Genome Biol. 2025 Feb 28. 26(1): 44
    CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis.
    Xue Yang, Li Cheng, Ye Xin, Jianxiang Zhang, Xinfeng Chen, Jinchao Xu, Mengli Zhang, Ruopeng Feng, Judith Hyle, Wenjie Qi, Wojciech Rosikiewicz, Beisi Xu, Chunliang Li, Peng Xu.
       BACKGROUND: CTCF is considered as the most essential transcription factor regulating chromatin architecture and gene expression. However, genome-wide impact of CTCF on erythropoiesis has not been extensively investigated.
    RESULTS: Using a state-of-the-art human erythroid progenitor cell model (HUDEP-2 and HEL cell lines), we systematically investigate the effects of acute CTCF loss by an auxin-inducible degron system on transcriptional programs, chromatin accessibility, CTCF genome occupancy, and genome architecture. By integrating multi-omics datasets, we reveal that acute CTCF loss notably disrupts genome-wide chromatin accessibility and the transcription network. We detect over thousands of decreased chromatin accessibility regions but only a few hundred increased regions after CTCF depletion in HUDEP-2 and HEL lines, suggesting the role of CTCF in maintaining proper chromatin openness in the erythroid lineage. CTCF depletion in the erythroid context notably disrupts the boundary integrity of topologically associating domains and chromatin loops but does not affect nuclear compartmentalization. We find erythroid lineage-specific genes, including some metabolism-related genes, are suppressed at immature and mature stages. Notably, we find a subset of genes whose transcriptional levels increase upon CTCF depletion, accompanied by decreased chromatin accessibility regions enriched with the GATA motif. We further decipher the molecular mechanism underlying the CTCF/GATA2 repression axis through distal non-coding chromatin regions. These results suggest a suppressive role of CTCF in gene expression during erythroid lineage specification.
    CONCLUSIONS: Our study reveals a novel role of CTCF in regulating erythroid differentiation by maintaining its proper chromatin openness and gene expression network, which extends our understanding of CTCF biology.
    Keywords:  CTCF; Chromatin accessibility; Erythropoiesis; Genome editing; Hematopoiesis; Transcription regulation
    DOI:  https://doi.org/10.1186/s13059-025-03510-z
  2. Nat Commun. 2025 Mar 06. 16(1): 2235
    Structure-function relationship of ASH1L and histone H3K36 and H3K4 methylation.
    Kendra R Vann, Rajal Sharma, Chih-Chao Hsu, Maeva Devoucoux, Adam H Tencer, Lei Zeng, Kevin Lin, Li Zhu, Qin Li, Catherine Lachance, Ruben Rosas Ospina, Qiong Tong, Ka Lung Cheung, Shuai Yang, Soumi Biswas, Hongwen Xuan, Jovylyn Gatchalian, Lorena Alamillo, Jianlong Wang, Suk Min Jang, Brianna J Klein, Yue Lu, Patricia Ernst, Brian D Strahl, Scott B Rothbart, Martin J Walsh, Michael L Cleary, Jacques Côté, Xiaobing Shi, Ming-Ming Zhou, Tatiana G Kutateladze.
      The histone H3K36-specific methyltransferase ASH1L plays a critical role in development and is frequently dysregulated in human diseases, particularly cancer. Here, we report on the biological functions of the C-terminal region of ASH1L encompassing a bromodomain (ASH1LBD), a plant homeodomain (ASH1LPHD) finger, and a bromo-adjacent homology (ASH1LBAH) domain, structurally characterize these domains, describe their mechanisms of action, and explore functional crosstalk between them. We find that ASH1LPHD recognizes H3K4me2/3, whereas the neighboring ASH1LBD and ASH1LBAH have DNA binding activities. The DNA binding function of ASH1LBAH is a driving force for the association of ASH1L with the linker DNA in the nucleosome, and the large interface with ASH1LPHD stabilizes the ASH1LBAH fold, merging two domains into a single module. We show that ASH1L is involved in embryonic stem cell differentiation and co-localizes with H3K4me3 but not with H3K36me2 at transcription start sites of target genes and genome wide, and that the interaction of ASH1LPHD with H3K4me3 is inhibitory to the H3K36me2-specific catalytic activity of ASH1L. Our findings shed light on the mechanistic details by which the C-terminal domains of ASH1L associate with chromatin and regulate the enzymatic function of ASH1L.
    DOI:  https://doi.org/10.1038/s41467-025-57556-5
  3. Sci Adv. 2025 Mar 07. 11(10): eadu0577
    Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome.
    Masahiro Naganuma, Tomoya Kujirai, Haruhiko Ehara, Tamami Uejima, Tomoko Ito, Mie Goto, Mari Aoki, Masami Henmi, Sayako Miyamoto-Kohno, Mikako Shirouzu, Hitoshi Kurumizaka, Shun-Ichi Sekine.
      The metazoan transcription elongation complex (EC) of RNA polymerase II (RNAPII) generally stalls between the transcription start site and the first (+1) nucleosome. This promoter-proximal pausing involves negative elongation factor (NELF), 5,6-dichloro-1-β-d-ribobenzimidazole sensitivity-inducing factor (DSIF), and transcription elongation factor IIS (TFIIS) and is critical for subsequent productive transcription elongation. However, the detailed pausing mechanism and the involvement of the +1 nucleosome remain enigmatic. Here, we report cryo-electron microscopy structures of ECs stalled on nucleosomal DNA. In the absence of TFIIS, the EC is backtracked/arrested due to conflicts between NELF and the nucleosome. We identified two alternative binding modes of NELF, one of which reveals a critical contact with the downstream DNA through the conserved NELF-E basic helix. Upon binding with TFIIS, the EC progressed to the nucleosome to establish a paused EC with a partially unwrapped nucleosome. This paused EC strongly restricts EC progression further downstream. These structures illuminate the mechanism of RNAPII pausing/stalling at the +1 nucleosome.
    DOI:  https://doi.org/10.1126/sciadv.adu0577
  4. Nat Commun. 2025 Mar 04. 16(1): 2187
    Distinct gene regulatory dynamics drive skeletogenic cell fate convergence during vertebrate embryogenesis.
    Menghan Wang, Ana Di Pietro-Torres, Christian Feregrino, Maëva Luxey, Chloé Moreau, Sabrina Fischer, Antoine Fages, Danilo Ritz, Patrick Tschopp.
      Cell type repertoires have expanded extensively in metazoan animals, with some clade-specific cells being crucial to evolutionary success. A prime example are the skeletogenic cells of vertebrates. Depending on anatomical location, these cells originate from three different precursor lineages, yet they converge developmentally towards similar cellular phenotypes. Furthermore, their 'skeletogenic competency' arose at distinct evolutionary timepoints, thus questioning to what extent different skeletal body parts rely on truly homologous cell types. Here, we investigate how lineage-specific molecular properties are integrated at the gene regulatory level, to allow for skeletogenic cell fate convergence. Using single-cell functional genomics, we find that distinct transcription factor profiles are inherited from the three precursor states and incorporated at lineage-specific enhancer elements. This lineage-specific regulatory logic suggests that these regionalized skeletogenic cells are distinct cell types, rendering them amenable to individualized selection, to define adaptive morphologies and biomaterial properties in different parts of the vertebrate skeleton.
    DOI:  https://doi.org/10.1038/s41467-025-57480-8
  5. Cell Rep. 2025 Mar 05. pii: S2211-1247(25)00133-0. [Epub ahead of print]44(3): 115362
    PRC1 and PRC2 proximal interactome in mouse embryonic stem cells.
    Dick W Zijlmans, Suzan Stelloo, Danique Bax, Yavor Yordanov, Pien Toebosch, Maximilian W D Raas, Sigrid Verhelst, Lieke A Lamers, Marijke P A Baltissen, Pascal W T C Jansen, Guido van Mierlo, Maarten Dhaenens, Hendrik Marks, Michiel Vermeulen.
      Polycomb repressive complexes PRC1 and PRC2 control lineage-specific gene silencing during early embryogenesis. To better understand Polycomb biology, we profile the proximal interactome (proxeome) of multiple PRC1 and PRC2 subunits in mouse embryonic stem cells (mESCs). This analysis identifies >100 proteins proximal to PRC1 and PRC2, including transcription factors and RNA-binding proteins. Notably, approximately half of the PRC2 interactors overlap with PRC1. Pluripotency-associated factors, including NANOG, colocalize with PRC2 at specific genomic sites. Following PRC2 disruption, NANOG relocalizes to other genomic regions. Interestingly, we identify PRC1 members in PRC2 proxeomes but not reciprocally. This suggests that PRC1 and PRC2 may have independent functions in addition to their cooperative roles in establishing H3K27me3-marked chromatin domains. Finally, we compare PRC2 proxeomes across different cellular contexts, including ground-state mESCs, serum-cultured mESCs, and embryoid bodies. These analyses provide a comprehensive resource, enhancing our understanding of Polycomb biology and its dynamic role across developmental states.
    Keywords:  CP: Molecular biology; PRC1; PRC2; TurboID; embryonic development; polycomb chromatin domains; proteomics; proximity labeling; transcription factors
    DOI:  https://doi.org/10.1016/j.celrep.2025.115362
  6. EMBO J. 2025 Feb 28.
    Ubiquitous MEIS transcription factors actuate lineage-specific transcription to establish cell fate.
    Zoulfia Darieva, Peyman Zarrineh, Naomi Phillips, Joshua Mallen, Araceli Garcia Mora, Ian Donaldson, Laure Bridoux, Megan Douglas, Sara F Dias Henriques, Dorothea Schulte, Matthew J Birket, Nicoletta Bobola.
      Control of gene expression is commonly mediated by distinct combinations of transcription factors (TFs). This cooperative action allows the integration of multiple biological signals at regulatory elements, resulting in highly specific gene expression patterns. It is unclear whether combinatorial binding is also necessary to bring together TFs with distinct biochemical functions, which collaborate to effectively recruit and activate RNA polymerase II. Using a cardiac differentiation model, we find that the largely ubiquitous homeodomain proteins MEIS act as actuators, fully activating transcriptional programs selected by lineage-restricted TFs. Combinatorial binding of MEIS with lineage-enriched TFs, GATA, and HOX, provides selectivity, guiding MEIS to function at cardiac-specific enhancers. In turn, MEIS TFs promote the accumulation of the methyltransferase KMT2D to initiate lineage-specific enhancer commissioning. MEIS combinatorial binding dynamics, dictated by the changing dosage of its partners, drive cells into progressive stages of differentiation. Our results uncover tissue-specific transcriptional activation as the result of ubiquitous actuator TFs harnessing general transcriptional activator at tissue-specific enhancers, to which they are directed by binding with lineage- and domain-specific TFs.
    Keywords:  Cardiac Differentiation; Combinatorial Binding; Transcription Factors
    DOI:  https://doi.org/10.1038/s44318-025-00385-5
  7. Nat Struct Mol Biol. 2025 Mar 03.
    ZBTB16/PLZF regulates juvenile spermatogonial stem cell development through an extensive transcription factor poising network.
    Chongil Yi, Yuka Kitamura, So Maezawa, Satoshi H Namekawa, Bradley R Cairns.
      Spermatogonial stem cells balance self-renewal with differentiation and spermatogenesis to ensure continuous sperm production. Here, we identify roles for the transcription factor zinc finger and BTB domain-containing protein 16 (ZBTB16; also known as promyelocytic leukemia zinc finger (PLZF)) in juvenile mouse undifferentiated spermatogonia (uSPG) in promoting self-renewal and cell-cycle progression to maintain uSPG and transit-amplifying states. Notably, ZBTB16, Spalt-like transcription factor 4 (SALL4) and SRY-box transcription factor 3 (SOX3) colocalize at over 12,000 promoters regulating uSPG and meiosis. These regions largely share broad histone 3 methylation and acetylation (H3K4me3 and H3K27ac), DNA hypomethylation, RNA polymerase II (RNAPol2) and often CCCTC-binding factor (CTCF). Hi-C analyses show robust three-dimensional physical interactions among these cobound promoters, suggesting the existence of a transcription factor and higher-order active chromatin interaction network within uSPG that poises meiotic promoters for subsequent activation. Conversely, these factors do not notably occupy germline-specific promoters driving spermiogenesis, which instead lack promoter-promoter physical interactions and bear DNA hypermethylation, even when active. Overall, ZBTB16 promotes uSPG cell-cycle progression and colocalizes with SALL4, SOX3, CTCF and RNAPol2 to help establish an extensive and interactive chromatin poising network.
    DOI:  https://doi.org/10.1038/s41594-025-01509-5
  8. Nat Commun. 2025 Mar 04. 16(1): 2181
    CODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to regulate the histone supply.
    Tae-Kyeong Jeong, R Ciaran MacKenzie Frater, Jongha Yoon, Anja Groth, Ji-Joon Song.
      ASF1 is a major histone chaperone that regulates the supply of histone H3-H4 and facilitates nucleosome assembly to maintain chromatin structure during DNA replication and transcription. CODANIN-1 negatively regulates the function of ASF1. However, the molecular mechanism by which CODANIN-1 inhibits the ASF1-mediated histone supply remains elusive. Here, we present the cryo-EM structure of a human CODANIN-1_ASF1A complex at 3.75 Å resolution. The structure reveals that CODANIN-1 forms a dimer where each monomer holds two ASF1 molecules, utilizing two B-domains and two histone H3 mimic helices (HMHs). The interaction of CODANIN-1 with ASF1 via the HMH and B-domains inhibits the formation of an ASF1/H3-H4 complex and sequesters ASF1 in the cytoplasm. Our study provides a structural and molecular basis for the function of CODANIN-1 as negative regulator that highjacks ASF1 interaction sites with histones and downstream chaperones to inhibit nucleosome assembly.
    DOI:  https://doi.org/10.1038/s41467-025-56976-7
  9. Cell Genom. 2025 Feb 20. pii: S2666-979X(25)00036-9. [Epub ahead of print] 100780
    Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage.
    Sahin Naqvi, Seungsoo Kim, Saman Tabatabaee, Anusri Pampari, Anshul Kundaje, Jonathan K Pritchard, Joanna Wysocka.
      Deep learning models have advanced our ability to predict cell-type-specific chromatin patterns from transcription factor (TF) binding motifs, but their application to perturbed contexts remains limited. We applied transfer learning to predict how concentrations of the dosage-sensitive TFs TWIST1 and SOX9 affect regulatory element (RE) chromatin accessibility in facial progenitor cells, achieving near-experimental accuracy. High-affinity motifs that allow for heterotypic TF co-binding and are concentrated at the center of REs buffer against quantitative changes in TF dosage and predict unperturbed accessibility. Conversely, low-affinity or homotypic binding motifs distributed throughout REs drive sensitive responses with minimal impact on unperturbed accessibility. Both buffering and sensitizing features display purifying selection signatures. We validated these sequence features through reporter assays and demonstrated that TF-nucleosome competition can explain low-affinity motifs' sensitizing effects. This combination of transfer learning and quantitative chromatin response measurements provides a novel approach for uncovering additional layers of the cis-regulatory code.
    Keywords:  chromatin accessibility; deep learning; degrons; gene dosage; gene regulation; motif affinity; nucleosomes; transcription factors
    DOI:  https://doi.org/10.1016/j.xgen.2025.100780
  10. Nat Commun. 2025 Mar 03. 16(1): 2148
    Interplay between CTCF-binding and CTCF-lacking regulatory elements in generating an architectural stripe at the Igh locus.
    Fei Ma, Noah Ollikainen, Hansen Du, Fatima Zohra Braikia, Nina Cui, Aisha Haley Bianchi, Christopher Dunn, Cuong Nguyen, Jinshui Fan, Supriyo De, Ranjan Sen, Xiang Qiu.
      Three-dimensional genome organization orchestrates recombination and transcription of immunoglobulin heavy chain (Igh) genes. The structure of wild-type (WT) alleles includes a prominent architectural stripe that extends from a cluster of CTCF binding elements at the 3' end of the locus (3'CBE), suggesting interactions of this end with sequences throughout the 2 Mb Igh TAD. Here we elucidate interplay between regulatory elements located in the 3'Igh domain (260 kb) that impact the stripe. The CTCF-lacking intronic enhancer, Eµ, promotes stripe formation and tethers sub-TADs between flanking CTCF-bound 3'CBE and IGCR1. Substituting Eµ with an EF1α promoter in different orientations partially recapitulates epigenetic features of WT Igh alleles, including active histone modifications, sub-TAD formation and interactions with the 3'CBE, but does not restore VDJ recombination. Loss of IGCR1 increases the stripe while inverting the 3'CBE redirects the stripe away from the Igh locus. However, inverted 3'CBE continue to serve as a boundary against aberrant activation of genes outside the Igh domain by Eµ. Our observations provide insights into mechanisms by which regulatory elements modulate chromatin structure and stripe formation.
    DOI:  https://doi.org/10.1038/s41467-025-57373-w
  11. Nat Struct Mol Biol. 2025 Mar 03.
    CTCF-mediated 3D chromatin sets up the gene expression program in the male germline.
    Yuka Kitamura, Kazuki Takahashi, So Maezawa, Yasuhisa Munakata, Akihiko Sakashita, Shawna P Katz, Noam Kaplan, Satoshi H Namekawa.
      Spermatogenesis is a unidirectional differentiation process that generates haploid sperm, but how the gene expression program that directs this process is established is largely unknown. Here we determine the high-resolution three-dimensional (3D) chromatin architecture of mouse male germ cells during spermatogenesis and show that CTCF-mediated 3D chromatin dictates the gene expression program required for spermatogenesis. In undifferentiated spermatogonia, CTCF-mediated chromatin interactions between meiosis-specific super-enhancers (SEs) and their target genes precede activation of these SEs on autosomes. These meiotic SEs recruit the master transcription factor A-MYB (MYBL1) in meiotic spermatocytes, which strengthens their 3D contacts and instructs a burst of meiotic gene expression. We also find that at the mitosis-to-meiosis transition, the germline-specific Polycomb protein SCML2 facilitates the resolution of chromatin loops that are specific to mitotic spermatogonia. Moreover, SCML2 and A-MYB help shape the unique 3D chromatin organization of sex chromosomes during meiotic sex chromosome inactivation. We propose that CTCF-mediated 3D chromatin organization regulates epigenetic priming that directs unidirectional differentiation, thereby determining the cellular identity of the male germline.
    DOI:  https://doi.org/10.1038/s41594-025-01482-z
  12. Sci Adv. 2025 Feb 28. 11(9): eadu6799
    Increased levels of lagging strand polymerase α in an adult stem cell lineage affect replication-coupled histone incorporation.
    Brendon E M Davis, Jonathan Snedeker, Rajesh Ranjan, Matthew Wooten, Savannah Sáde Barton, Joshua Blundon, Xin Chen.
      Stem cells display asymmetric histone inheritance, while nonstem progenitor cells exhibit symmetric patterns in the Drosophila male germ line. Here, we report that components involved in lagging strand synthesis, DNA polymerases α and δ, have substantially reduced levels in stem cells compared to progenitor cells, and this promotes local asymmetry of parental histone incorporation at the replication fork. Compromising Polα genetically induces the local replication-coupled histone incorporation pattern in progenitor cells to resemble that in stem cells, seen by both nuclear localization patterns and chromatin fibers. This is recapitulated using a Polα inhibitor in a concentration-dependent manner. The local old versus new histone asymmetry is comparable between stem cells and progenitor cells at both S phase and M phase. Together, these results indicate that developmentally programmed expression of key DNA replication components is important to shape stem cell chromatin. Furthermore, manipulating one crucial DNA replication component can induce replication-coupled histone dynamics in nonstem cells to resemble those in stem cells.
    DOI:  https://doi.org/10.1126/sciadv.adu6799
  13. Cell Genom. 2025 Feb 27. pii: S2666-979X(25)00062-X. [Epub ahead of print] 100806
    Capturing cell-type-specific activities of cis-regulatory elements from peak-based single-cell ATAC-seq.
    Mengjie Chen.
      Single-cell ATAC sequencing (scATAC-seq), a state-of-the-art genomic technique designed to map chromatin accessibility at the single-cell level, presents unique analytical challenges due to limited sampling and data sparsity. In this study, we use case studies to highlight the limitations of conventional peak-based methods for processing scATAC-seq data. These methods can fail to capture precise cell-type-specific regulatory signals, producing results that are difficult to interpret and lack portability, thereby compromising the reproducibility of research findings. To overcome these issues, we introduce CREscendo, a method that utilizes Tn5 cleavage frequencies and regulatory annotations to identify differential usage of candidate regulatory elements (CREs) across cell types. Our research advocates for moving away from traditional peak-based quantification in scATAC-seq toward a more robust framework that relies on a standardized reference of annotated CREs, enhancing both the accuracy and reproducibility of genomic studies.
    Keywords:  cis-regulatory element; gene activities; peak calling; scATAC-seq; single cell
    DOI:  https://doi.org/10.1016/j.xgen.2025.100806
  14. Genome Res. 2025 Mar 03.
    Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements.
    Hosiana Abewe, Alexandra Richey, Jeffery M Vahrenkamp, Matthew Ginley-Hidinger, Craig M Rush, Noel Kitchen, Xiaoyang Zhang, Jason Gertz.
      Transcriptional enhancers can regulate individual or multiple genes through long-range three-dimensional (3D) genome interactions, and these interactions are commonly altered in cancer. Yet, the functional relationship between changes in 3D genome interactions associated with regulatory regions and differential gene expression appears context-dependent. In this study, we used HiChIP to capture changes in 3D genome interactions between active regulatory regions of endometrial cancer cells in response to estrogen treatment and uncovered significant differential long-range interactions strongly enriched for estrogen receptor alpha (ER, also known as ESR1)-bound sites (ERBSs). The ERBSs anchoring differential chromatin loops with either a gene's promoter or distal regions were correlated with larger transcriptional responses to estrogen compared with ERBSs not involved in differential 3D genome interactions. To functionally test this observation, CRISPR-based Enhancer-i was used to deactivate specific ERBSs, which revealed a wide range of effects on the transcriptional response to estrogen. However, these effects are only subtly and not significantly stronger for ERBSs in differential chromatin loops. In addition, we observed an enrichment of 3D genome interactions between the promoters of estrogen-upregulated genes and found that looped promoters can work together cooperatively. Overall, our work reveals that estrogen treatment causes large changes in 3D genome structure in endometrial cancer cells; however, these changes are not required for a regulatory region to contribute to an estrogen transcriptional response.
    DOI:  https://doi.org/10.1101/gr.279699.124
  15. Sci Adv. 2025 Feb 28. 11(9): eadr9660
    TFIIH kinase CDK7 drives cell proliferation through a common core transcription factor network.
    Taylor Jones, Junjie Feng, Olivia Luyties, Kira Cozzolino, Lynn Sanford, Jenna K Rimel, Christopher C Ebmeier, Grace S Shelby, Lotte P Watts, Jessica Rodino, Nisha Rajagopal, Shanhu Hu, Finn Brennan, Zachary L Maas, Sydney Alnemy, William F Richter, Adrian F Koh, Nora B Cronin, Ameya Madduri, Jhuma Das, Elliot Cooper, Kristin B Hamman, John P Carulli, Mary A Allen, Sabrina Spencer, Abhay Kotecha, Jason J Marineau, Basil J Greber, Robin D Dowell, Dylan J Taatjes.
      How cyclin-dependent kinase 7 (CDK7) coordinately regulates the cell cycle and RNA polymerase II transcription remains unclear. Here, high-resolution cryo-electron microscopy revealed how two clinically relevant inhibitors block CDK7 function. In cells, CDK7 inhibition rapidly suppressed transcription, but constitutively active genes were disproportionately affected versus stimulus-responsive. Distinct transcription factors (TFs) regulate constitutive versus stimulus-responsive genes. Accordingly, stimulus-responsive TFs were refractory to CDK7 inhibition whereas constitutively active "core" TFs were repressed. Core TFs (n = 78) are predominantly promoter associated and control cell cycle and proliferative gene expression programs across cell types. Mechanistically, rapid suppression of core TF function can occur through CDK7-dependent phosphorylation changes in core TFs and RB1. Moreover, CDK7 inhibition depleted core TF protein levels within hours, consistent with durable target gene suppression. Thus, a major but unappreciated biological function for CDK7 is regulation of a TF cohort that drives proliferation, revealing an apparent universal mechanism by which CDK7 coordinates RNAPII transcription with cell cycle CDK regulation.
    DOI:  https://doi.org/10.1126/sciadv.adr9660
  16. Mol Cell. 2025 Feb 25. pii: S1097-2765(25)00133-9. [Epub ahead of print]
    Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.
    Lizhen Wu, Anurupa Devi Yadavalli, Filip Senigl, Gabriel Matos-Rodrigues, Dijin Xu, Andreas P Pintado-Urbanc, Matthew D Simon, Wei Wu, André Nussenzweig, David G Schatz.
      Somatic hypermutation (SHM) and class switch recombination (CSR) diversify immunoglobulin (Ig) genes and are initiated by the activation-induced deaminase (AID), a single-stranded DNA cytidine deaminase thought to engage its substrate during RNA polymerase II (RNAPII) transcription. Through a genetic screen, we identified numerous potential factors involved in SHM, including elongation factor 1 homolog (ELOF1), a component of the RNAPII elongation complex that functions in transcription-coupled nucleotide excision repair (TC-NER) and transcription elongation. Loss of ELOF1 compromises SHM, CSR, and AID action in mammalian B cells and alters RNAPII transcription by reducing RNAPII pausing downstream of transcription start sites and levels of serine 5 but not serine 2 phosphorylated RNAPII throughout transcribed genes. ELOF1 must bind to RNAPII to be a proximity partner for AID and to function in SHM and CSR, and TC-NER is not required for SHM. We propose that ELOF1 helps create the appropriate stalled RNAPII substrate on which AID acts.
    Keywords:  AID; ELOF1; RNA polymerase II; class switch recombination; somatic hypermutation; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2025.02.007
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