bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2024–10–27
twenty-six papers selected by
Connor Rogerson, University of Cambridge
  1. Transcription-dependent mobility of single genes and genome-wide motions in live human cells.
  2. Spt5 orchestrates cryptic transcript suppression and transcriptional directionality.
  3. DNA methylation shapes the Polycomb landscape during the exit from naive pluripotency.
  4. Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships.
  5. The homeodomain regulates stable DNA binding of prostate cancer target ONECUT2.
  6. Targeting the transcription factor YY1 is synthetic lethal with loss of the histone demethylase KDM5C.
  7. Chromatin remodelling drives immune cell-fibroblast communication in heart failure.
  8. Machine-guided design of cell-type-targeting cis-regulatory elements.
  9. Conserved helical motifs in the IKZF1 disordered region mediate NuRD interaction and transcriptional repression.
  10. USP10 drives cancer stemness and enables super-competitor signalling in colorectal cancer.
  11. Single-cell multi-modal integrative analyses highlight functional dynamic gene regulatory networks directing human cardiac development.
  12. Tetrameric INTS6-SOSS1 complex facilitates DNA:RNA hybrid autoregulation at double-strand breaks.
  13. Characterization of Medusavirus encoded histones reveals nucleosome-like structures and a unique linker histone.
  14. SRSF2 safeguards efficient transcription of DNA damage and repair genes.
  15. TASOR expression in naive embryonic stem cells safeguards their developmental potential.
  16. Light-induced targeting enables proteomics on endogenous condensates.
  17. H3K14ac facilitates the reinstallation of constitutive heterochromatin in Drosophila early embryos by engaging Eggless/SetDB1.
  18. Dependence of PAX3-FOXO1 chromatin occupancy on ETS1 at important disease-promoting genes exposes new targetable vulnerability in Fusion-Positive Rhabdomyosarcoma.
  19. Predicting protein synergistic effect in Arabidopsis using epigenome profiling.
  20. Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development.
  21. Generation of human expandable limb-bud-like progenitors via chemically induced dedifferentiation.
  22. Uncoupling of mTORC1 from E2F activity maintains DNA damage and senescence.
  23. PRC2-EZH1 contributes to circadian gene expression by orchestrating chromatin states and RNA polymerase II complex stability.
  24. iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia.
  25. Epigenetic modulation via the C-terminal tail of H2A.Z.
  26. EMBRYONIC FLOWER 1 regulates male reproduction by repressing the jasmonate pathway downstream transcription factor MYB26.
  1. Nat Commun. 2024 Oct 22. 15(1): 8879
    Transcription-dependent mobility of single genes and genome-wide motions in live human cells.
    Fang-Yi Chu, Alexis S Clavijo, Suho Lee, Alexandra Zidovska.
      The human genome is highly dynamic across all scales. At the gene level, chromatin is persistently remodeled and rearranged during active processes such as transcription, replication and DNA repair. At the genome level, chromatin moves in micron-scale domains that break up and re-form over seconds, but the origin of these coherent motions is unknown. Here, we investigate the connection between genomic motions and gene-level activity. Simultaneous mapping of single-gene and genome-wide motions shows that the coupling of gene transcriptional activity to flows of the nearby genome is modulated by chromatin compaction. A motion correlation analysis suggests that a single active gene drives larger-scale motions in low-compaction regions, but high-compaction chromatin drives gene motion regardless of its activity state. By revealing unexpected connections among gene activity, spatial heterogeneities of chromatin and its emergent genome-wide motions, these findings uncover aspects of the genome's spatiotemporal organization that directly impact gene regulation and expression.
    DOI:  https://doi.org/10.1038/s41467-024-51149-4
  2. Commun Biol. 2024 Oct 22. 7(1): 1370
    Spt5 orchestrates cryptic transcript suppression and transcriptional directionality.
    Haejin An, Hyeokjun Yang, Daeyoup Lee.
      Spt5 is a well-conserved factor that manipulates multiple stages of transcription from promoter-proximal pausing (PPP) to termination. Recent studies have revealed an unexpected increase of antisense transcripts near promoters in cells expressing mutant Spt5. Here, we identify Spt5p-restricted intragenic antisense transcripts and their close relationship with sense transcription in yeast. We confirm that Spt5 CTR phosphorylation is also important to retain Spt5's facility to regulate antisense transcription. The genes whose antisense transcription is strongly suppressed by Spt5p share strong endogenous sense transcription and weak antisense transcription, and this pattern is conserved in humans. Mechanistically, we found that Spt5p depletion increased histone acetylation to initiate intragenic antisense transcription by altering chromatin structure. We additionally identified termination factors that appear to be involved in the ability of Spt5p to restrict antisense transcription. By unveiling a new role of Spt5 in finely balancing the bidirectionality of transcription, we demonstrate that Spt5-mediated suppression of DSIF complex regulated-unstable transcripts (DUTs) is essential to sustain the accurate transcription by RNA polymerase II.
    DOI:  https://doi.org/10.1038/s42003-024-07014-7
  3. Nat Struct Mol Biol. 2024 Oct 24.
    DNA methylation shapes the Polycomb landscape during the exit from naive pluripotency.
    Julien Richard Albert, Teresa Urli, Ana Monteagudo-Sánchez, Anna Le Breton, Amina Sultanova, Angélique David, Margherita Scarpa, Mathieu Schulz, Maxim V C Greenberg.
      In mammals, 5-methylcytosine (5mC) and Polycomb repressive complex 2 (PRC2)-deposited histone 3 lysine 27 trimethylation (H3K27me3) are generally mutually exclusive at CpG-rich regions. As mouse embryonic stem cells exit the naive pluripotent state, there is massive gain of 5mC concomitantly with restriction of broad H3K27me3 to 5mC-free, CpG-rich regions. To formally assess how 5mC shapes the H3K27me3 landscape, we profiled the epigenome of naive and differentiated cells in the presence and absence of the DNA methylation machinery. Surprisingly, we found that 5mC accumulation is not required to restrict most H3K27me3 domains. Instead, this 5mC-independent H3K27me3 restriction is mediated by aberrant expression of the PRC2 antagonist Ezhip (encoding EZH inhibitory protein). At the subset of regions where 5mC appears to genuinely supplant H3K27me3, we identified 163 candidate genes that appeared to require 5mC deposition and/or H3K27me3 depletion for their activation in differentiated cells. Using site-directed epigenome editing to directly modulate 5mC levels, we demonstrated that 5mC deposition is sufficient to antagonize H3K27me3 deposition and confer gene activation at individual candidates. Altogether, we systematically measured the antagonistic interplay between 5mC and H3K27me3 in a system that recapitulates early embryonic dynamics. Our results suggest that H3K27me3 restraint depends on 5mC, both directly and indirectly. Our study also implies a noncanonical role of 5mC in gene activation, which may be important not only for normal development but also for cancer progression, as oncogenic cells frequently exhibit dynamic replacement of 5mC for H3K27me3 and vice versa.
    DOI:  https://doi.org/10.1038/s41594-024-01405-4
  4. Genome Res. 2024 Oct 22. pii: gr.279037.124. [Epub ahead of print]
    Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships.
    Michelle Kudron, Louis Gewirtzman, Alec Victorsen, Bridget C Lear, Dionne Vafeados, Jiahao Gao, Jinrui Xu, Swapna Samanta, Emily Frink, Adri Tran-Pearson, Chau Hyunh, Ann Hammonds, William Fisher, Martha L Wall, Greg Wesseling, Vanessa Hernandez, Zhichun Lin, Mary Kasparian, Kevin P White, Ravi Allada, Mark Gerstein, LaDeana Hillier, Susan E Celniker, Valerie Reinke, Robert Waterston.
      A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here we present the culmination of the efforts of the Model Organism ENCyclopedia Of DNA Elements (modENCODE) and the model organism Encyclopedia of Regulatory Networks (modERN) consortia to systematically assay TF binding events in vivo in two major model organisms, Drosophila melanogaster (fly) and Caenorhabditis elegans (worm). These datasets comprise 605 TFs identifying 3.6M sites in the fly and 356 TFs identifying 0.9 M sites in the worm and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed "metapeaks", that larger metapeaks have characteristics of high occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single cell RNA-seq data in a machine learning model identifies TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent-daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing GFP-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell type-specific TF-target relationships.
    DOI:  https://doi.org/10.1101/gr.279037.124
  5. Nat Commun. 2024 Oct 19. 15(1): 9037
    The homeodomain regulates stable DNA binding of prostate cancer target ONECUT2.
    Avradip Chatterjee, Brad Gallent, Madhusudhanarao Katiki, Chen Qian, Matthew R Harter, Steve Silletti, Elizabeth A Komives, Michael R Freeman, Ramachandran Murali.
      The CUT and homeodomain are ubiquitous DNA binding elements often tandemly arranged in multiple transcription factor families. However, how the CUT and homeodomain work concertedly to bind DNA remains unknown. Using ONECUT2, a driver and therapeutic target of advanced prostate cancer, we show that while the CUT initiates DNA binding, the homeodomain thermodynamically stabilizes the ONECUT2-DNA complex through allosteric modulation of CUT. We identify an arginine pair in the ONECUT family homeodomain that can adapt to DNA sequence variations. Base interactions by this ONECUT family-specific arginine pair as well as the evolutionarily conserved residues are critical for optimal DNA binding and ONECUT2 transcriptional activity in a prostate cancer model. The evolutionarily conserved base interactions additionally determine the ONECUT2-DNA binding energetics. These findings provide insights into the cooperative DNA binding by CUT-homeodomain proteins.
    DOI:  https://doi.org/10.1038/s41467-024-53159-8
  6. EMBO Rep. 2024 Oct 21.
    Targeting the transcription factor YY1 is synthetic lethal with loss of the histone demethylase KDM5C.
    Qian Zheng, Pengfei Li, Yulong Qiang, Jiachen Fan, Yuzhu Xing, Ying Zhang, Fan Yang, Feng Li, Jie Xiong.
      An understanding of the enzymatic and scaffolding functions of epigenetic modifiers is important for the development of epigenetic therapies for cancer. The H3K4me2/3 histone demethylase KDM5C has been shown to regulate transcription. The diverse roles of KDM5C are likely determined by its interacting partners, which are still largely unknown. In this study, we screen for KDM5C-binding proteins and show that YY1 interacts with KDM5C. A synergistic antitumor effect is exerted when both KDM5C and YY1 are depleted, and targeting YY1 appears to be a vulnerability in KDM5C-deficient cancer cells. Mechanistically, KDM5C promotes global YY1 chromatin recruitment, especially at promoters. Moreover, an intact KDM5C JmjC domain but not KDM5C histone demethylase activity is required for KDM5C-mediated YY1 chromatin binding. Transcriptional profiling reveals that dual inhibition of KDM5C and YY1 increases transcriptional repression of cell cycle- and apoptosis-related genes. In summary, our work demonstrates a synthetic lethal interaction between YY1 and KDM5C and suggests combination therapies for cancer treatments.
    Keywords:  Cancer Therapy; Chromatin Recruitment; KDM5C; Promoter; YY1
    DOI:  https://doi.org/10.1038/s44319-024-00290-8
  7. Nature. 2024 Oct 23.
    Chromatin remodelling drives immune cell-fibroblast communication in heart failure.
    Michael Alexanian, Arun Padmanabhan, Tomohiro Nishino, Joshua G Travers, Lin Ye, Angelo Pelonero, Clara Youngna Lee, Nandhini Sadagopan, Yu Huang, Kirsten Auclair, Ada Zhu, Yuqian An, Christina A Ekstrand, Cassandra Martinez, Barbara Gonzalez Teran, Will R Flanigan, Charis Kee-Seon Kim, Koya Lumbao-Conradson, Zachary Gardner, Li Li, Mauro W Costa, Rajan Jain, Israel Charo, Alexis J Combes, Saptarsi M Haldar, Katherine S Pollard, Ronald J Vagnozzi, Timothy A McKinsey, Pawel F Przytycki, Deepak Srivastava.
      Chronic inflammation and tissue fibrosis are common responses that worsen organ function, yet the molecular mechanisms governing their cross-talk are poorly understood. In diseased organs, stress-induced gene expression changes fuel maladaptive cell state transitions1 and pathological interaction between cellular compartments. Although chronic fibroblast activation worsens dysfunction in the lungs, liver, kidneys and heart, and exacerbates many cancers2, the stress-sensing mechanisms initiating transcriptional activation of fibroblasts are poorly understood. Here we show that conditional deletion of the transcriptional co-activator Brd4 in infiltrating Cx3cr1+ macrophages ameliorates heart failure in mice and significantly reduces fibroblast activation. Analysis of single-cell chromatin accessibility and BRD4 occupancy in vivo in Cx3cr1+ cells identified a large enhancer proximal to interleukin-1β (IL-1β, encoded by Il1b), and a series of CRISPR-based deletions revealed the precise stress-dependent regulatory element that controls Il1b expression. Secreted IL-1β activated a fibroblast RELA-dependent (also known as p65) enhancer near the transcription factor MEOX1, resulting in a profibrotic response in human cardiac fibroblasts. In vivo, antibody-mediated IL-1β neutralization improved cardiac function and tissue fibrosis in heart failure. Systemic IL-1β inhibition or targeted Il1b deletion in Cx3cr1+ cells prevented stress-induced Meox1 expression and fibroblast activation. The elucidation of BRD4-dependent cross-talk between a specific immune cell subset and fibroblasts through IL-1β reveals how inflammation drives profibrotic cell states and supports strategies that modulate this process in heart disease and other chronic inflammatory disorders featuring tissue remodelling.
    DOI:  https://doi.org/10.1038/s41586-024-08085-6
  8. Nature. 2024 Oct 23.
    Machine-guided design of cell-type-targeting cis-regulatory elements.
    Sager J Gosai, Rodrigo I Castro, Natalia Fuentes, John C Butts, Kousuke Mouri, Michael Alasoadura, Susan Kales, Thanh Thanh L Nguyen, Ramil R Noche, Arya S Rao, Mary T Joy, Pardis C Sabeti, Steven K Reilly, Ryan Tewhey.
      Cis-regulatory elements (CREs) control gene expression, orchestrating tissue identity, developmental timing and stimulus responses, which collectively define the thousands of unique cell types in the body1-3. While there is great potential for strategically incorporating CREs in therapeutic or biotechnology applications that require tissue specificity, there is no guarantee that an optimal CRE for these intended purposes has arisen naturally. Here we present a platform to engineer and validate synthetic CREs capable of driving gene expression with programmed cell-type specificity. We take advantage of innovations in deep neural network modelling of CRE activity across three cell types, efficient in silico optimization and massively parallel reporter assays to design and empirically test thousands of CREs4-8. Through large-scale in vitro validation, we show that synthetic sequences are more effective at driving cell-type-specific expression in three cell lines compared with natural sequences from the human genome and achieve specificity in analogous tissues when tested in vivo. Synthetic sequences exhibit distinct motif vocabulary associated with activity in the on-target cell type and a simultaneous reduction in the activity of off-target cells. Together, we provide a generalizable framework to prospectively engineer CREs from massively parallel reporter assay models and demonstrate the required literacy to write fit-for-purpose regulatory code.
    DOI:  https://doi.org/10.1038/s41586-024-08070-z
  9. Blood. 2024 Oct 22. pii: blood.2024024787. [Epub ahead of print]
    Conserved helical motifs in the IKZF1 disordered region mediate NuRD interaction and transcriptional repression.
    Tianyi Zhang, Yi-Fang Wang, Alex Montoya, Ilinca Patrascan, Nehir Nebioglu, Husayn A Pallikonda, Radina Georgieva, James Wd King, Holger B Kramer, Pavel V Shliaha, David S Rueda, Matthias Merkenschlager.
      The transcription factor IKZF1 is essential for B cell development, and recurrently mutated in human B-ALL. IKZF1 has been ascribed both activating and repressive functions via interactions with coactivator and corepressor complexes, but the relative abundance of IKZF1-associated coregulators and their contribution to IKZF1-mediated gene regulation are not well understood. To address this, we performed an unbiased identification of IKZF1-interacting proteins in pre-B cells and found that IKZF1 interacts overwhelmingly with corepressors and heterochromatin-associated proteins. Time-resolved analysis of transcription and chromatin state identified transcriptional repression as the immediate response to IKZF1 induction. Transcriptional repression preceded transcriptional activation by several hours, manifesting as a decrease in the fraction of transcriptional bursts at the single molecule level. Repression was accompanied by a rapid loss of chromatin accessibility and reduced levels of H3K27ac particularly at enhancers. We identified highly conserved helical motifs within the intrinsically disordered region in IKZF1 that mediate its association with the NuRD corepressor complex through critical "KRK" residues that bind the NuRD subunit RBBP4, a mechanism shared with the TFs FOG1, BCL11A, and SALL4. Functional characterization reveals this region is necessary for to the efficient silencing of target genes and antiproliferative functions of IKZF1 in B-ALL.
    DOI:  https://doi.org/10.1182/blood.2024024787
  10. Oncogene. 2024 Oct 23.
    USP10 drives cancer stemness and enables super-competitor signalling in colorectal cancer.
    Michaela Reissland, Oliver Hartmann, Saskia Tauch, Jeroen M Bugter, Cristian Prieto-Garcia, Clemens Schulte, Sinah Loebbert, Daniel Solvie, Eliya Bitman-Lotan, Ashwin Narain, Anne-Claire Jacomin, Christina Schuelein-Voelk, Carmina T Fuss, Nikolett Pahor, Carsten Ade, Viktoria Buck, Michael Potente, Vivian Li, Gerti Beliu, Armin Wiegering, Tom Grossmann, Martin Eilers, Elmar Wolf, Hans Maric, Mathias Rosenfeldt, Madelon M Maurice, Ivan Dikic, Peter Gallant, Amir Orian, Markus E Diefenbacher.
      The contribution of deubiquitylating enzymes (DUBs) to β-Catenin stabilization in intestinal stem cells and colorectal cancer (CRC) is poorly understood. Here, and by using an unbiassed screen, we discovered that the DUB USP10 stabilizes β-Catenin specifically in APC-truncated CRC in vitro and in vivo. Mechanistic studies, including in vitro binding together with computational modelling, revealed that USP10 binding to β-Catenin is mediated via the unstructured N-terminus of USP10 and is outcompeted by intact APC, favouring β-catenin degradation. However, in APC-truncated cancer cells USP10 binds to β-catenin, increasing its stability which is critical for maintaining an undifferentiated tumour identity. Elimination of USP10 reduces the expression of WNT and stem cell signatures and induces the expression of differentiation genes. Remarkably, silencing of USP10 in murine and patient-derived CRC organoids established that it is essential for NOTUM signalling and the APC super competitor-phenotype, reducing tumorigenic properties of APC-truncated CRC. These findings are clinically relevant as patient-derived organoids are highly dependent on USP10, and abundance of USP10 correlates with poorer prognosis of CRC patients. Our findings reveal, therefore, a role for USP10 in CRC cell identity, stemness, and tumorigenic growth by stabilising β-Catenin, leading to aberrant WNT signalling and degradation resistant tumours. Thus, USP10 emerges as a unique therapeutic target in APC truncated CRC.
    DOI:  https://doi.org/10.1038/s41388-024-03141-x
  11. Cell Genom. 2024 Oct 16. pii: S2666-979X(24)00299-4. [Epub ahead of print] 100680
    Single-cell multi-modal integrative analyses highlight functional dynamic gene regulatory networks directing human cardiac development.
    Alyssa R Holman, Shaina Tran, Eugin Destici, Elie N Farah, Ting Li, Aileena C Nelson, Adam J Engler, Neil C Chi.
      Illuminating the precise stepwise genetic programs directing cardiac development provides insights into the mechanisms of congenital heart disease and strategies for cardiac regenerative therapies. Here, we integrate in vitro and in vivo human single-cell multi-omic studies with high-throughput functional genomic screening to reveal dynamic, cardiac-specific gene regulatory networks (GRNs) and transcriptional regulators during human cardiomyocyte development. Interrogating developmental trajectories reconstructed from single-cell data unexpectedly reveal divergent cardiomyocyte lineages with distinct gene programs based on developmental signaling pathways. High-throughput functional genomic screens identify key transcription factors from inferred GRNs that are functionally relevant for cardiomyocyte lineages derived from each pathway. Notably, we discover a critical heat shock transcription factor 1 (HSF1)-mediated cardiometabolic GRN controlling cardiac mitochondrial/metabolic function and cell survival, also observed in fetal human cardiomyocytes. Overall, these multi-modal genomic studies enable the systematic discovery and validation of coordinated GRNs and transcriptional regulators controlling the development of distinct human cardiomyocyte populations.
    Keywords:  CRISPR-based functional genomics screening; cardiac development; directed differentiation; gene regulatory networks; multi-omics
    DOI:  https://doi.org/10.1016/j.xgen.2024.100680
  12. Nucleic Acids Res. 2024 Oct 24. pii: gkae937. [Epub ahead of print]
    Tetrameric INTS6-SOSS1 complex facilitates DNA:RNA hybrid autoregulation at double-strand breaks.
    Qilin Long, Kamal Ajit, Katerina Sedova, Vojtech Haluza, Richard Stefl, Sadat Dokaneheifard, Felipe Beckedorff, Monica G Valencia, Marek Sebesta, Ramin Shiekhattar, Monika Gullerova.
      DNA double-strand breaks (DSBs) represent a lethal form of DNA damage that can trigger cell death or initiate oncogenesis. The activity of RNA polymerase II (RNAPII) at the break site is required for efficient DSB repair. However, the regulatory mechanisms governing the transcription cycle at DSBs are not well understood. Here, we show that Integrator complex subunit 6 (INTS6) associates with the heterotrimeric sensor of ssDNA (SOSS1) complex (comprising INTS3, INIP and hSSB1) to form the tetrameric SOSS1 complex. INTS6 binds to DNA:RNA hybrids and promotes Protein Phosphatase 2A (PP2A) recruitment to DSBs, facilitating the dephosphorylation of RNAPII. Furthermore, INTS6 prevents the accumulation of damage-associated RNA transcripts (DARTs) and the stabilization of DNA:RNA hybrids at DSB sites. INTS6 interacts with and promotes the recruitment of senataxin (SETX) to DSBs, facilitating the resolution of DNA:RNA hybrids/R-loops. Our results underscore the significance of the tetrameric SOSS1 complex in the autoregulation of DNA:RNA hybrids and efficient DNA repair.
    DOI:  https://doi.org/10.1093/nar/gkae937
  13. Nat Commun. 2024 Oct 23. 15(1): 9138
    Characterization of Medusavirus encoded histones reveals nucleosome-like structures and a unique linker histone.
    Chelsea M Toner, Nicole M Hoitsma, Sashi Weerawarana, Karolin Luger.
      The organization of DNA into nucleosomes is a ubiquitous and ancestral feature that was once thought to be exclusive to the eukaryotic domain of life. Intriguingly, several representatives of the Nucleocytoplasmic Large DNA Viruses (NCLDV) encode histone-like proteins that in Melbournevirus were shown to form nucleosome-like particles. Medusavirus medusae (MM), a distantly related giant virus, encodes all four core histone proteins and, unique amongst most giant viruses, a putative acidic protein with two domains resembling eukaryotic linker histone H1. Here, we report the structure of nucleosomes assembled with MM histones and highlight similarities and differences with eukaryotic and Melbournevirus nucleosomes. Our structure provides insight into how variations in histone tail and loop lengths are accommodated within the context of the nucleosome. We show that MM-histones assemble into tri-nucleosome arrays, and that the putative linker histone H1 does not function in chromatin compaction. These findings expand our limited understanding of chromatin organization by virus-encoded histones.
    DOI:  https://doi.org/10.1038/s41467-024-53364-5
  14. Cell Rep. 2024 Oct 23. pii: S2211-1247(24)01220-8. [Epub ahead of print]43(11): 114869
    SRSF2 safeguards efficient transcription of DNA damage and repair genes.
    Rebecca E Wagner, Leonie Arnetzl, Thiago Britto-Borges, Anke Heit-Mondrzyk, Ali Bakr, Etienne Sollier, Nikoletta A Gkatza, Jasper Panten, Sylvain Delaunay, Daniela Sohn, Peter Schmezer, Duncan T Odom, Karin Müller-Decker, Christoph Plass, Christoph Dieterich, Pavlo Lutsik, Susanne Bornelöv, Michaela Frye.
      The serine-/arginine-rich splicing factor 2 (SRSF2) plays pivotal roles in pre-mRNA processing and gene transcription. Recurrent mutations, particularly a proline-to-histidine substitution at position 95 (P95H), are common in neoplastic diseases. Here, we assess SRSF2's diverse functions in squamous cell carcinoma. We show that SRSF2 deletion or homozygous P95H mutation both cause extensive DNA damage leading to cell-cycle arrest. Mechanistically, SRSF2 regulates efficient bi-directional transcription of DNA replication and repair genes, independent from its function in splicing. Further, SRSF2 haploinsufficiency induces DNA damage without halting the cell cycle. Exposing mouse skin to tumor-promoting carcinogens enhances the clonal expansion of heterozygous Srsf2 P95H epidermal cells but unexpectedly inhibits tumor formation. To survive carcinogen treatment, Srsf2 P95H+/- cells undergo substantial transcriptional rewiring and restore bi-directional gene expression. Thus, our study underscores SRSF2's importance in regulating transcription to orchestrate the cell cycle and the DNA damage response.
    Keywords:  CP: Cancer; CP: Molecular biology; DNA damage; DNA repair; DNA replication; Transcription; bi-directional promoters; epithelia; skin
    DOI:  https://doi.org/10.1016/j.celrep.2024.114869
  15. Cell Rep. 2024 Oct 24. pii: S2211-1247(24)01238-5. [Epub ahead of print]43(11): 114887
    TASOR expression in naive embryonic stem cells safeguards their developmental potential.
    Carlos A Pinzon-Arteaga, Ryan O'Hara, Alice Mazzagatti, Emily Ballard, Yingying Hu, Alex Pan, Daniel A Schmitz, Yulei Wei, Masahiro Sakurai, Peter Ly, Laura A Banaszynski, Jun Wu.
      The seamless transition through stages of pluripotency relies on a balance between transcription factor networks and epigenetic mechanisms. Here, we reveal the crucial role of the transgene activation suppressor (TASOR), a component of the human silencing hub (HUSH) complex, in maintaining cell viability during the transition from naive to primed pluripotency. TASOR loss in naive pluripotent stem cells (PSCs) triggers replication stress, disrupts H3K9me3 heterochromatin, and impairs silencing of LINE-1 (L1) transposable elements, with more severe effects in primed PSCs. Notably, the survival of Tasor knockout PSCs during this transition can be restored by inhibiting caspase or deleting the mitochondrial antiviral signaling protein (MAVS). This suggests that unscheduled L1 expression activates an innate immune response, leading to cell death specifically in cells exiting naive pluripotency. Our findings highlight the importance of epigenetic programs established in naive pluripotency for normal development.
    Keywords:  5mC; CP: Stem cell research; DNA methylation; H3K9me3; HUSH complex; L1; LINE-1; Stem cells; TASOR; heterochromatin; naive pluripotency; primed pluripotency
    DOI:  https://doi.org/10.1016/j.celrep.2024.114887
  16. Cell. 2024 Oct 15. pii: S0092-8674(24)01140-1. [Epub ahead of print]
    Light-induced targeting enables proteomics on endogenous condensates.
    Choongman Lee, Andrea Quintana, Ida Suppanz, Alejandro Gomez-Auli, Gerhard Mittler, Ibrahim I Cissé.
      Endogenous condensates with transient constituents are notoriously difficult to study with common biological assays like mass spectrometry and other proteomics profiling. Here, we report a method for light-induced targeting of endogenous condensates (LiTEC) in living cells. LiTEC combines the identification of molecular zip codes that target the endogenous condensates with optogenetics to enable controlled and reversible partitioning of an arbitrary cargo, such as enzymes commonly used in proteomics, into the condensate in a blue light-dependent manner. We demonstrate a proof of concept by combining LiTEC with proximity-based biotinylation (BioID) and uncover putative components of transcriptional condensates in mouse embryonic stem cells. Our approach opens the road to genome-wide functional studies of endogenous condensates.
    Keywords:  IDR; LiTEC; composition; endogenous condensate; intrinsically disordered; mass spectrometry; optogenetics; proteomics; targeting; transcriptional cluster
    DOI:  https://doi.org/10.1016/j.cell.2024.09.040
  17. Proc Natl Acad Sci U S A. 2024 Aug 13. 121(33): e2321859121
    H3K14ac facilitates the reinstallation of constitutive heterochromatin in Drosophila early embryos by engaging Eggless/SetDB1.
    Ruijun Tang, Mengqi Zhou, Yuwei Chen, Zhenghui Jiang, Xunan Fan, Jingheng Zhang, Aiping Dong, Lu Lv, Song Mao, Fang Chen, Guanjun Gao, Jinrong Min, Ke Liu, Kai Yuan.
      Constitutive heterochromatin, a fundamental feature of eukaryotic nucleus essential for transposon silencing and genome stability, is rebuilt on various types of repetitive DNA in the zygotic genome during early embryogenesis. However, the molecular program underlying this process remains poorly understood. Here, we show that histone H3 lysine 14 acetylation (H3K14ac) is engaged in the reinstallation of constitutive heterochromatin in Drosophila early embryos. H3K14ac partially colocalizes with H3 lysine 9 trimethylation (H3K9me3) and its methyltransferase Eggless/SetDB1 around the mid-blastula transition. Concealing H3K14ac by either antibody injection or maternal knockdown of Gcn5 diminishes Eggless/SetDB1 nuclear foci and reduces the deposition of H3K9me3. Structural analysis reveals that Eggless/SetDB1 recognizes H3K14ac via its tandem Tudor domains, and disrupting the binding interface causes defects in Eggless/SetDB1 distribution and derepression of a subset of transposons. Therefore, H3K14ac, a histone modification normally associated with active transcription, is a crucial component of the early embryonic machinery that introduces constitutive heterochromatic features to the newly formed zygotic genome.
    Keywords:  Drosophila; Eggless/SetDB1; H3K14ac; early embryo; heterochromatin
    DOI:  https://doi.org/10.1073/pnas.2321859121
  18. Oncogene. 2024 Oct 24.
    Dependence of PAX3-FOXO1 chromatin occupancy on ETS1 at important disease-promoting genes exposes new targetable vulnerability in Fusion-Positive Rhabdomyosarcoma.
    Joseph Hsieh, Etienne P Danis, Charles R Owens, Janet K Parrish, Nathan L Nowling, Arthur R Wolin, Stephen Connor Purdy, Sheera R Rosenbaum, Atma M Ivancevic, Edward B Chuong, Heide L Ford, Paul Jedlicka.
      Rhabdomyosarcoma (RMS), a malignancy of impaired myogenic differentiation, is the most common soft tissue pediatric cancer. PAX3-FOXO1 oncofusions drive the majority of the clinically more aggressive fusion-positive rhabdomyosarcoma (FP-RMS). Recent studies have established an epigenetic basis for PAX3-FOXO1-driven oncogenic processes. However, details of PAX3-FOXO1 epigenetic mechanisms, including interactions with, and dependence on, other chromatin and transcription factors, are incompletely understood. We previously identified a novel disease-promoting epigenetic axis in RMS, involving the histone demethylase KDM3A and the ETS1 transcription factor, and demonstrated that this epigenetic axis interfaces with PAX3-FOXO1 both phenotypically and transcriptomically, including co-regulation of biological processes and genes important to FP-RMS progression. In this study, we demonstrate that KDM3A and ETS1 colocalize with PAX3-FOXO1 to enhancers of important disease-promoting genes in FP-RMS, including FGF8, IL4R, and MEST, as well as PODXL, which we define herein as a new FP-RMS-promoting gene. We show that ETS1, which is induced by both PAX3-FOXO1 and KDM3A, exists in complex with PAX3-FOXO1, and augments PAX3-FOXO1 chromatin occupancy. We further show that the PAX3-FOXO1/ETS1 complex can be disrupted by the clinically relevant small molecule inhibitor YK-4-279. YK-4-279 displaces PAX3-FOXO1 from chromatin and interferes with PAX3-FOXO1-dependent gene regulation, resulting in potent inhibition of growth and invasive properties in FP-RMS, along with downregulation of FGF8, IL4R, MEST and PODXL expression. We additionally show that, in some FP-RMS, KDM3A also increases PAX3-FOXO1 levels. Together, our studies illuminate mechanisms of action of the KDM3A/ETS1 regulatory module, and reveal novel targetable mechanisms of PAX3-FOXO1 chromatin complex regulation, in FP-RMS.
    DOI:  https://doi.org/10.1038/s41388-024-03201-2
  19. Nat Commun. 2024 Oct 24. 15(1): 9160
    Predicting protein synergistic effect in Arabidopsis using epigenome profiling.
    Chih-Hung Hsieh, Ya-Ting Sabrina Chang, Ming-Ren Yen, Jo-Wei Allison Hsieh, Pao-Yang Chen.
      Histone modifications can regulate transcription epigenetically by marking specific genomic loci, which can be mapped using chromatin immunoprecipitation sequencing (ChIP-seq). Here we present QHistone, a predictive database of 1534 ChIP-seqs from 27 histone modifications in Arabidopsis, offering three key functionalities. Firstly, QHistone employs machine learning to predict the epigenomic profile of a query protein, characterized by its most associated histone modifications, and uses these modifications to infer the protein's role in transcriptional regulation. Secondly, it predicts synergistic regulatory activities between two proteins by comparing their profiles. Lastly, it detects previously unexplored co-regulating protein pairs by screening all known proteins. QHistone accurately identifies histone modifications associated with specific known proteins, and allows users to computationally validate their results using gene expression data from various plant tissues. These functions demonstrate an useful approach to utilizing epigenome data for gene regulation analysis, making QHistone a valuable resource for the scientific community ( https://qhistone.paoyang.ipmb.sinica.edu.tw ).
    DOI:  https://doi.org/10.1038/s41467-024-53565-y
  20. Genome Res. 2024 Oct 21. pii: gr.278344.123. [Epub ahead of print]
    Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development.
    Song Zhang, Chao Wang, Shenghua Qin, Choulin Chen, Yongzhou Bao, Yuanyuan Zhang, Lingna Xu, Qingyou Liu, Yunxiang Zhao, Kui Li, Zhonglin Tang, Yuwen Liu.
      Super-enhancers (SEs) govern the expression of genes defining cell identity. However, the dynamic landscape of SEs and their critical constituent enhancers involved in skeletal muscle development remains unclear. In this study, using pig as a model, we employed CUT&Tag to profile the enhancer-associated histone modification marker H3K27ac in skeletal muscle across two prenatal and three postnatal stages and investigated how SEs influence skeletal muscle development. We identified three SE families with distinct temporal dynamics: continuous (Con, 397), transient (TS, 434), and de novo (DN, 756). These SE families are associated with different temporal gene expression trajectories, biological functions, and DNA methylation levels. Notably, several lines of evidence suggest a potential prominent role of Con SEs in regulating porcine muscle development and meat traits. To pinpoint key cis-regulatory units in Con SEs, we developed an integrative approach that leverages information from eRNA annotation, GWAS signals and high-throughput capture STARR-seq experiments. Within Con SEs, we identified 20 candidate critical enhancers with meat and carcass-associated DNA variations that affect enhancer activity and inferred their upstream TFs and downstream target genes. As a proof of concept, we experimentally validated the role of one such enhancer and its potential target gene during myogenesis. Our findings reveal the dynamic regulatory features of SEs in skeletal muscle development and provide a general integrative framework for identifying critical enhancers underlying the formation of complex traits.
    DOI:  https://doi.org/10.1101/gr.278344.123
  21. Cell Stem Cell. 2024 Oct 16. pii: S1934-5909(24)00363-1. [Epub ahead of print]
    Generation of human expandable limb-bud-like progenitors via chemically induced dedifferentiation.
    Jialiang Zhu, Xinxing Zhong, Huanjing He, Jingxiao Cao, Zhengyang Zhou, Jiebin Dong, Honggang Li, Anqi Zhang, Yulin Lyu, Cheng Li, Jingyang Guan, Hongkui Deng.
      In certain highly regenerative animals, cellular dedifferentiation occurs after injury, allowing specialized cells to become progenitor cells for regeneration. However, this capacity is restricted in human cells due to reduced plasticity. Here, we introduce a chemical-induced dedifferentiation approach that reverts the differentiated cells to a progenitor-like state, conferring the features of human limb bud cells from human adult somatic cells. These chemically induced human limb-bud-like progenitors (hCiLBP cells) show a high degree of transcriptomic similarity to human embryonic limb bud progenitors. Importantly, we established culture conditions that allow hCiLBP cells to undergo extensive expansion while maintaining population homogeneity and long-term self-renewal capacity. Moreover, hCiLBP cells exhibit increased osteochondrogenic differentiation ability, providing an innovative platform for generation of skeletal lineage cell types. These results highlight a potential therapeutic approach for repairing damaged human tissues through reversal of developmental pathways from mature cells to expandable progenitor cells.
    Keywords:  chemical reprogramming; dedifferentiation; human limb-bud-like progenitors; large-scale expansion; progenitor maintenance; regeneration
    DOI:  https://doi.org/10.1016/j.stem.2024.10.001
  22. Nat Commun. 2024 Oct 24. 15(1): 9181
    Uncoupling of mTORC1 from E2F activity maintains DNA damage and senescence.
    Leighton H Daigh, Debarya Saha, David L Rosenthal, Katherine R Ferrick, Tobias Meyer.
      DNA damage is a primary trigger for cellular senescence, which in turn causes organismal aging and is a promising target of anti-aging therapies. Most DNA damage occurs when DNA is fragile during DNA replication in S phase, but senescent cells maintain DNA damage long-after DNA replication has stopped. How senescent cells induce DNA damage and why senescent cells fail to repair damaged DNA remain open questions. Here, we combine reversible expression of the senescence-inducing CDK4/6 inhibitory protein p16INK4 (p16) with live single-cell analysis and show that sustained mTORC1 signaling triggers senescence in non-proliferating cells by increasing transcriptional DNA damage and inflammation signaling that persists after p16 is degraded. Strikingly, we show that activation of E2F transcriptional program, which is regulated by CDK4/6 activity and promotes expression of DNA repair proteins, repairs transcriptionally damaged DNA without requiring DNA replication. Together, our study suggests that senescence can be maintained by ongoing mTORC1-induced transcriptional DNA damage that cannot be sufficiently repaired without induction of protective E2F target genes.
    DOI:  https://doi.org/10.1038/s41467-024-52820-6
  23. EMBO J. 2024 Oct 21.
    PRC2-EZH1 contributes to circadian gene expression by orchestrating chromatin states and RNA polymerase II complex stability.
    Peng Liu, Seba Nadeef, Maged F Serag, Andreu Paytuví-Gallart, Maram Abadi, Francesco Della Valle, Santiago Radío, Xènia Roda, Jaïr Dilmé Capó, Sabir Adroub, Nadine Hosny El Said, Bodor Fallatah, Mirko Celii, Gian Marco Messa, Mengge Wang, Mo Li, Paola Tognini, Lorena Aguilar-Arnal, Satoshi Habuchi, Selma Masri, Paolo Sassone-Corsi, Valerio Orlando.
      Circadian rhythmicity of gene expression is a conserved feature of cell physiology. This involves fine-tuning between transcriptional and post-transcriptional mechanisms and strongly depends on the metabolic state of the cell. Together these processes guarantee an adaptive plasticity of tissue-specific genetic programs. However, it is unclear how the epigenome and RNA Pol II rhythmicity are integrated. Here we show that the PcG protein EZH1 has a gateway bridging function in postmitotic skeletal muscle cells. On the one hand, the circadian clock master regulator BMAL1 directly controls oscillatory behavior and periodic assembly of core components of the PRC2-EZH1 complex. On the other hand, EZH1 is essential for circadian gene expression at alternate Zeitgeber times, through stabilization of RNA Polymerase II preinitiation complexes, thereby controlling nascent transcription. Collectively, our data show that PRC2-EZH1 regulates circadian transcription both negatively and positively by modulating chromatin states and basal transcription complex stability.
    Keywords:  Circadian Rhythm; EZH1; H3K27me3; Transcription
    DOI:  https://doi.org/10.1038/s44318-024-00267-2
  24. PLoS Comput Biol. 2024 Oct 23. 20(10): e1012546
    iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia.
    Anand V Sastry, Yuan Yuan, Saugat Poudel, Kevin Rychel, Reo Yoo, Cameron R Lamoureux, Gaoyuan Li, Joshua T Burrows, Siddharth Chauhan, Zachary B Haiman, Tahani Al Bulushi, Yara Seif, Bernhard O Palsson, Daniel C Zielinski.
      Public gene expression databases are a rapidly expanding resource of organism responses to diverse perturbations, presenting both an opportunity and a challenge for bioinformatics workflows to extract actionable knowledge of transcription regulatory network function. Here, we introduce a five-step computational pipeline, called iModulonMiner, to compile, process, curate, analyze, and characterize the totality of RNA-seq data for a given organism or cell type. This workflow is centered around the data-driven computation of co-regulated gene sets using Independent Component Analysis, called iModulons, which have been shown to have broad applications. As a demonstration, we applied this workflow to generate the iModulon structure of Bacillus subtilis using all high-quality, publicly-available RNA-seq data. Using this structure, we predicted regulatory interactions for multiple transcription factors, identified groups of co-expressed genes that are putatively regulated by undiscovered transcription factors, and predicted properties of a recently discovered single-subunit phage RNA polymerase. We also present a Python package, PyModulon, with functions to characterize, visualize, and explore computed iModulons. The pipeline, available at https://github.com/SBRG/iModulonMiner, can be readily applied to diverse organisms to gain a rapid understanding of their transcriptional regulatory network structure and condition-specific activity.
    DOI:  https://doi.org/10.1371/journal.pcbi.1012546
  25. Nat Commun. 2024 Oct 24. 15(1): 9171
    Epigenetic modulation via the C-terminal tail of H2A.Z.
    László Imre, Péter Nánási, Ibtissem Benhamza, Kata Nóra Enyedi, Gábor Mocsár, Rosevalentine Bosire, Éva Hegedüs, Erfaneh Firouzi Niaki, Ágota Csóti, Zsuzsanna Darula, Éva Csősz, Szilárd Póliska, Beáta Scholtz, Gábor Mező, Zsolt Bacsó, H T Marc Timmers, Masayuki Kusakabe, Margit Balázs, György Vámosi, Juan Ausio, Peter Cheung, Katalin Tóth, David Tremethick, Masahiko Harata, Gábor Szabó.
      H2A.Z-nucleosomes are present in both euchromatin and heterochromatin and it has proven difficult to interpret their disparate roles in the context of their stability features. Using an in situ assay of nucleosome stability and DT40 cells expressing engineered forms of the histone variant we show that native H2A.Z, but not C-terminally truncated H2A.Z (H2A.Z∆C), is released from nucleosomes of peripheral heterochromatin at unusually high salt concentrations. H2A.Z and H3K9me3 landscapes are reorganized in H2A.Z∆C-nuclei and overall sensitivity of chromatin to nucleases is increased. These tail-dependent differences are recapitulated upon treatment of HeLa nuclei with the H2A.Z-tail-peptide (C9), with MNase sensitivity being increased genome-wide. Fluorescence correlation spectroscopy revealed C9 binding to reconstituted nucleosomes. When introduced into live cells, C9 elicited chromatin reorganization, overall nucleosome destabilization and changes in gene expression. Thus, H2A.Z-nucleosomes influence global chromatin architecture in a tail-dependent manner, what can be modulated by introducing the tail-peptide into live cells.
    DOI:  https://doi.org/10.1038/s41467-024-53514-9
  26. Plant Cell. 2024 Oct 22. pii: koae287. [Epub ahead of print]
    EMBRYONIC FLOWER 1 regulates male reproduction by repressing the jasmonate pathway downstream transcription factor MYB26.
    Zhijuan Chen, Jing Lu, Xiaoyi Li, Danhua Jiang, Zicong Li.
      The evolutionarily conserved Polycomb repressive complexes (PRC) mediate genome-wide transcriptional silencing and regulate a plethora of development, as well as environmental responses in multicellular organisms. The PRC2-catalyzed trimethylation of lysine 27 on histone H3 (H3K27me3) is recognized by reader-effector modules of PRC1 to implement gene repression. Here, we report that the Arabidopsis (Arabidopsis thaliana) H3K27me3 effector EMBRYONIC FLOWER 1 (EMF1) interacts with and constrains the R2R3 DNA binding transcription factor MYB26 by a eudicot-conserved motif in the stamen. MYB26 activates the transcription of two NAC domain genes, NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) and NST2, whose encoded proteins mediate anther secondary cell thickening in jasmonate (JA)-regulated stamen maturation. In this process, the transcriptional activity of MYB26 is negatively modulated by the JAZ-PRC repressive complex to precisely regulate the expression of NST1 and NST2. Disruption of EMF1 repression stimulates MYB26, leading to the excessive transcription of the two NAC genes and male sterility. Our results reveal a novel mechanism in polycomb-mediated gene silencing and illustrate that the plant Polycomb complex regulates stamen development by preventing the hypersensitivity of JA responses in male reproduction.
    DOI:  https://doi.org/10.1093/plcell/koae287
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