bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2023‒07‒09
25 papers selected by
Connor Rogerson
University of Cambridge
  1. Chromatin regulation of transcriptional enhancers and cell fate by the Sotos syndrome gene NSD1.
  2. Different chromatin-scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2.
  3. Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin.
  4. TONSOKU is required for the maintenance of repressive chromatin modifications in Arabidopsis.
  5. Cooperation between bHLH transcription factors and histones for DNA access.
  6. Transcription factors interact with RNA to regulate genes.
  7. 3D chromatin reprogramming primes human memory TH2 cells for rapid recall and pathogenic dysfunction.
  8. FOXA2 controls the anti-oxidant response in FH-deficient cells.
  9. ZMYM2 is essential for methylation of germline genes and active transposons in embryonic development.
  10. Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies.
  11. A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2.
  12. Cancer lineage-specific regulation of YAP responsive elements revealed through large-scale functional epigenomic screens.
  13. Dynamic de novo heterochromatin assembly and disassembly at replication forks ensures fork stability.
  14. Characterizing the landscape of gene expression variance in humans.
  15. TET2 and TET3 loss disrupts small intestine differentiation and homeostasis.
  16. Structural insights into human TFIIIC promoter recognition.
  17. De novo detection of somatic mutations in high-throughput single-cell profiling data sets.
  18. Oncogenic K-Ras suppresses global miRNA function.
  19. Inducible disruption of Tet genes results in myeloid malignancy, readthrough transcription, and a heterochromatin-to-euchromatin switch.
  20. Single cohesin molecules generate force by two distinct mechanisms.
  21. Integration of gene expression and DNA methylation data across different experiments.
  22. Metabolic regulation of CTCF expression and chromatin association dictates starvation response in mice and flies.
  23. Sugar-responsive inhibition of Myc-dependent ribosome biogenesis by Clockwork orange.
  24. An EZH2-NF-κB regulatory axis drives expression of pro-oncogenic gene signatures in triple negative breast cancer.
  25. Cis-regulatory landscape size, constraint, and tissue-specificity associate with gene function and expression.
  1. Mol Cell. 2023 Jun 24. pii: S1097-2765(23)00430-6. [Epub ahead of print]
    Chromatin regulation of transcriptional enhancers and cell fate by the Sotos syndrome gene NSD1.
    Zhen Sun, Yuan Lin, Mohammed T Islam, Richard Koche, Lin Hedehus, Dingyu Liu, Chang Huang, Thomas Vierbuchen, Charles L Sawyers, Kristian Helin.
      Nuclear receptor-binding SET-domain protein 1 (NSD1), a methyltransferase that catalyzes H3K36me2, is essential for mammalian development and is frequently dysregulated in diseases, including Sotos syndrome. Despite the impacts of H3K36me2 on H3K27me3 and DNA methylation, the direct role of NSD1 in transcriptional regulation remains largely unknown. Here, we show that NSD1 and H3K36me2 are enriched at cis-regulatory elements, particularly enhancers. NSD1 enhancer association is conferred by a tandem quadruple PHD (qPHD)-PWWP module, which recognizes p300-catalyzed H3K18ac. By combining acute NSD1 depletion with time-resolved epigenomic and nascent transcriptomic analyses, we demonstrate that NSD1 promotes enhancer-dependent gene transcription by facilitating RNA polymerase II (RNA Pol II) pause release. Notably, NSD1 can act as a transcriptional coactivator independent of its catalytic activity. Moreover, NSD1 enables the activation of developmental transcriptional programs associated with Sotos syndrome pathophysiology and controls embryonic stem cell (ESC) multilineage differentiation. Collectively, we have identified NSD1 as an enhancer-acting transcriptional coactivator that contributes to cell fate transition and Sotos syndrome development.
    Keywords:  H3K36 methylation; NSD1; Pol II pause release; Sotos syndrome; chromatin; enhancers; gene expression; histone methylation; reader domain; stem cells
    DOI:  https://doi.org/10.1016/j.molcel.2023.06.007
  2. Cell Rep. 2023 Jul 04. pii: S2211-1247(23)00759-3. [Epub ahead of print]42(7): 112748
    Different chromatin-scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2.
    Jonathan Lerner, Andrew Katznelson, Jingchao Zhang, Kenneth S Zaret.
      Pioneer transcription factors interact with nucleosomes to scan silent, compact chromatin, enabling cooperative events that modulate gene activity. While at a subset of sites pioneer factors access chromatin by assisted loading with other transcription factors, the nucleosome-binding properties of pioneer factors enable them to initiate zygotic genome activation, embryonic development, and cellular reprogramming. To better understand nucleosome targeting in vivo, we assess whether pioneer factors FoxA1 and Sox2 target stable or unstable nucleosomes and find that they target DNase-resistant, stable nucleosomes, whereas HNF4A, a non-nucleosome binding factor, targets open, DNase-sensitive chromatin. Despite FOXA1 and SOX2 targeting similar proportions of DNase-resistant chromatin, using single-molecule tracking, we find that FOXA1 uses lower nucleoplasmic diffusion and longer residence times while SOX2 uses higher nucleoplasmic diffusion and shorter residence times to scan compact chromatin, while HNF4 scans compact chromatin much less efficiently. Thus, pioneer factors target compact chromatin through distinct processes.
    Keywords:  CP: Molecular biology; FOXA; HNF4; SOX2; chromatin; development; dynamics; gene networks; pioneer factor; reprogramming
    DOI:  https://doi.org/10.1016/j.celrep.2023.112748
  3. Science. 2023 Jul 07. 381(6653): 92-100
    Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin.
    Mark E Pownall, Liyun Miao, Charles E Vejnar, Ons M'Saad, Alice Sherrard, Megan A Frederick, Maria D J Benitez, Curtis W Boswell, Kenneth S Zaret, Joerg Bewersdorf, Antonio J Giraldez.
      Nanoscale chromatin organization regulates gene expression. Although chromatin is notably reprogrammed during zygotic genome activation (ZGA), the organization of chromatin regulatory factors during this universal process remains unclear. In this work, we developed chromatin expansion microscopy (ChromExM) to visualize chromatin, transcription, and transcription factors in vivo. ChromExM of embryos during ZGA revealed how the pioneer factor Nanog interacts with nucleosomes and RNA polymerase II (Pol II), providing direct visualization of transcriptional elongation as string-like nanostructures. Blocking elongation led to more Pol II particles clustered around Nanog, with Pol II stalled at promoters and Nanog-bound enhancers. This led to a new model termed "kiss and kick", in which enhancer-promoter contacts are transient and released by transcriptional elongation. Our results demonstrate that ChromExM is broadly applicable to study nanoscale nuclear organization.
    DOI:  https://doi.org/10.1126/science.ade5308
  4. Cell Rep. 2023 Jul 01. pii: S2211-1247(23)00749-0. [Epub ahead of print]42(7): 112738
    TONSOKU is required for the maintenance of repressive chromatin modifications in Arabidopsis.
    Lin Wang, Mande Xue, Huairen Zhang, Lijun Ma, Danhua Jiang.
      The stability of eukaryotic genomes relies on the faithful transmission of DNA sequences and the maintenance of chromatin states through DNA replication. Plant TONSOKU (TSK) and its animal ortholog TONSOKU-like (TONSL) act as readers for newly synthesized histones and preserve DNA integrity via facilitating DNA repair at post-replicative chromatin. However, whether TSK/TONSL regulate the maintenance of chromatin states remains elusive. Here, we show that TSK is dispensable for global histone and nucleosome accumulation but necessary for maintaining repressive chromatin modifications, including H3K9me2, H2A.W, H3K27me3, and DNA methylation. TSK physically interacts with H3K9 methyltransferases and Polycomb proteins. Moreover, TSK mutation strongly enhances defects in Polycomb pathway mutants. TSK is intended to only associate with nascent chromatin until it starts to mature. We propose that TSK ensures the preservation of chromatin states by supporting the recruitment of chromatin modifiers to post-replicative chromatin in a critical short window of time following DNA replication.
    Keywords:  CP: Molecular biology; CP: Plants; DNA methylation; H2A.W; H3K27 methylation; H3K9 methylation; chromatin; epigenetic inheritance; replication
    DOI:  https://doi.org/10.1016/j.celrep.2023.112738
  5. Nature. 2023 Jul 05.
    Cooperation between bHLH transcription factors and histones for DNA access.
    Alicia K Michael, Lisa Stoos, Priya Crosby, Nikolas Eggers, Xinyu Y Nie, Kristina Makasheva, Martina Minnich, Kelly L Healy, Joscha Weiss, Georg Kempf, Simone Cavadini, Lukas Kater, Jan Seebacher, Luca Vecchia, Deyasini Chakraborty, Luke Isbel, Ralph S Grand, Florian Andersch, Jennifer L Fribourgh, Dirk Schübeler, Johannes Zuber, Andrew C Liu, Peter B Becker, Beat Fierz, Carrie L Partch, Jerome S Menet, Nicolas H Thomä.
      The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members1. Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs. 2,3). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry-exit sites. Structural studies with engineered or native nucleosome sequences show that MYC-MAX or CLOCK-BMAL1 triggers the release of DNA from histones to gain access. Atop the H2A-H2B acidic patch4, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes5-7 at endogenous DNA sequences occurs through direct interactions between two CLOCK-BMAL1 protomers and histones and is important for circadian cycling. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B and H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerization domain jointly determine the histone contact, the affinity and the degree of competition and cooperativity with other nucleosome-bound factors.
    DOI:  https://doi.org/10.1038/s41586-023-06282-3
  6. Mol Cell. 2023 Jun 27. pii: S1097-2765(23)00434-3. [Epub ahead of print]
    Transcription factors interact with RNA to regulate genes.
    Ozgur Oksuz, Jonathan E Henninger, Robert Warneford-Thomson, Ming M Zheng, Hailey Erb, Adrienne Vancura, Kalon J Overholt, Susana Wilson Hawken, Salman F Banani, Richard Lauman, Lauren N Reich, Anne L Robertson, Nancy M Hannett, Tong I Lee, Leonard I Zon, Roberto Bonasio, Richard A Young.
      Transcription factors (TFs) orchestrate the gene expression programs that define each cell's identity. The canonical TF accomplishes this with two domains, one that binds specific DNA sequences and the other that binds protein coactivators or corepressors. We find that at least half of TFs also bind RNA, doing so through a previously unrecognized domain with sequence and functional features analogous to the arginine-rich motif of the HIV transcriptional activator Tat. RNA binding contributes to TF function by promoting the dynamic association between DNA, RNA, and TF on chromatin. TF-RNA interactions are a conserved feature important for vertebrate development and disrupted in disease. We propose that the ability to bind DNA, RNA, and protein is a general property of many TFs and is fundamental to their gene regulatory function.
    Keywords:  RNA; RNA-binding proteins; arginine-rich motif; chromatin; development; gene regulation; single-molecule imaging; transcription factor; zebrafish
    DOI:  https://doi.org/10.1016/j.molcel.2023.06.012
  7. Sci Immunol. 2023 Jul 14. 8(85): eadg3917
    3D chromatin reprogramming primes human memory TH2 cells for rapid recall and pathogenic dysfunction.
    Anne Onrust-van Schoonhoven, Marjolein J W de Bruijn, Bernard Stikker, Rutger W W Brouwer, Gert-Jan Braunstahl, Wilfred F J van IJcken, Thomas Graf, Danny Huylebroeck, Rudi W Hendriks, Grégoire Stik, Ralph Stadhouders.
      Memory T cells provide long-lasting defense responses through their ability to rapidly reactivate, but how they efficiently "recall" an inflammatory transcriptional program remains unclear. Here, we show that human CD4+ memory T helper 2 (TH2) cells carry a chromatin landscape synergistically reprogrammed at both one-dimensional (1D) and 3D levels to accommodate recall responses, which is absent in naive T cells. In memory TH2 cells, recall genes were epigenetically primed through the maintenance of transcription-permissive chromatin at distal (super)enhancers organized in long-range 3D chromatin hubs. Precise transcriptional control of key recall genes occurred inside dedicated topologically associating domains ("memory TADs"), in which activation-associated promoter-enhancer interactions were preformed and exploited by AP-1 transcription factors to promote rapid transcriptional induction. Resting memory TH2 cells from patients with asthma showed premature activation of primed recall circuits, linking aberrant transcriptional control of recall responses to chronic inflammation. Together, our results implicate stable multiscale reprogramming of chromatin organization as a key mechanism underlying immunological memory and dysfunction in T cells.
    DOI:  https://doi.org/10.1126/sciimmunol.adg3917
  8. Cell Rep. 2023 Jul 04. pii: S2211-1247(23)00762-3. [Epub ahead of print]42(7): 112751
    FOXA2 controls the anti-oxidant response in FH-deficient cells.
    Connor Rogerson, Marco Sciacovelli, Lucas A Maddalena, Andromachi Pouikli, Marc Segarra-Mondejar, Lorea Valcarcel-Jimenez, Christina Schmidt, Ming Yang, Elena Ivanova, Joshua Kent, Ariane Mora, Danya Cheeseman, Jason S Carroll, Gavin Kelsey, Christian Frezza.
      Hereditary leiomyomatosis and renal cell cancer (HLRCC) is a cancer syndrome caused by inactivating germline mutations in fumarate hydratase (FH) and subsequent accumulation of fumarate. Fumarate accumulation leads to profound epigenetic changes and the activation of an anti-oxidant response via nuclear translocation of the transcription factor NRF2. The extent to which chromatin remodeling shapes this anti-oxidant response is currently unknown. Here, we explored the effects of FH loss on the chromatin landscape to identify transcription factor networks involved in the remodeled chromatin landscape of FH-deficient cells. We identify FOXA2 as a key transcription factor that regulates anti-oxidant response genes and subsequent metabolic rewiring cooperating without direct interaction with the anti-oxidant regulator NRF2. The identification of FOXA2 as an anti-oxidant regulator provides additional insights into the molecular mechanisms behind cell responses to fumarate accumulation and potentially provides further avenues for therapeutic intervention for HLRCC.
    Keywords:  CP: Cancer; CP: Molecular biology; FOXA2; NRF2; anti-oxidant response; fumarate hydratase
    DOI:  https://doi.org/10.1016/j.celrep.2023.112751
  9. Nucleic Acids Res. 2023 Jul 03. pii: gkad540. [Epub ahead of print]
    ZMYM2 is essential for methylation of germline genes and active transposons in embryonic development.
    Adda-Lee Graham-Paquin, Deepak Saini, Jacinthe Sirois, Ishtiaque Hossain, Megan S Katz, Qinwei Kim-Wee Zhuang, Sin Young Kwon, Yojiro Yamanaka, Guillaume Bourque, Maxime Bouchard, William A Pastor.
      ZMYM2 is a transcriptional repressor whose role in development is largely unexplored. We found that Zmym2-/- mice show embryonic lethality by E10.5. Molecular characterization of Zmym2-/- embryos revealed two distinct defects. First, they fail to undergo DNA methylation and silencing of germline gene promoters, resulting in widespread upregulation of germline genes. Second, they fail to methylate and silence the evolutionarily youngest and most active LINE element subclasses in mice. Zmym2-/- embryos show ubiquitous overexpression of LINE-1 protein as well as aberrant expression of transposon-gene fusion transcripts. ZMYM2 homes to sites of PRC1.6 and TRIM28 complex binding, mediating repression of germline genes and transposons respectively. In the absence of ZMYM2, hypermethylation of histone 3 lysine 4 occurs at target sites, creating a chromatin landscape unfavourable for establishment of DNA methylation. ZMYM2-/- human embryonic stem cells also show aberrant upregulation and demethylation of young LINE elements, indicating a conserved role in repression of active transposons. ZMYM2 is thus an important new factor in DNA methylation patterning in early embryonic development.
    DOI:  https://doi.org/10.1093/nar/gkad540
  10. Sci Adv. 2023 Jul 07. 9(27): eade3399
    Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies.
    Keun Hong Son, Mark Borris D Aldonza, A-Reum Nam, Kang-Hoon Lee, Jeong-Woon Lee, Kyung-Ju Shin, Keunsoo Kang, Je-Yoel Cho.
      Dogs have become a valuable model in exploring multifaceted diseases and biology relevant to human health. Despite large-scale dog genome projects producing high-quality draft references, a comprehensive annotation of functional elements is still lacking. We addressed this through integrative next-generation sequencing of transcriptomes paired with five histone marks and DNA methylome profiling across 11 tissue types, deciphering the dog's epigenetic code by defining distinct chromatin states, super-enhancer, and methylome landscapes, and thus showed that these regions are associated with a wide range of biological functions and cell/tissue identity. In addition, we confirmed that the phenotype-associated variants are enriched in tissue-specific regulatory regions and, therefore, the tissue of origin of the variants can be traced. Ultimately, we delineated conserved and dynamic epigenomic changes at the tissue- and species-specific resolutions. Our study provides an epigenomic blueprint of the dog that can be used for comparative biology and medical research.
    DOI:  https://doi.org/10.1126/sciadv.ade3399
  11. Nat Commun. 2023 Jul 06. 14(1): 3993
    A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2.
    Marta Losa, Iros Barozzi, Marco Osterwalder, Viviana Hermosilla-Aguayo, Angela Morabito, Brandon H Chacón, Peyman Zarrineh, Ausra Girdziusaite, Jean Denis Benazet, Jianjian Zhu, Susan Mackem, Terence D Capellini, Diane Dickel, Nicoletta Bobola, Aimée Zuniga, Axel Visel, Rolf Zeller, Licia Selleri.
      A lingering question in developmental biology has centered on how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. Here, using the murine hindlimb as a model, we investigate the elusive mechanisms whereby PBX TALE homeoproteins, viewed primarily as HOX cofactors, attain context-specific developmental roles despite ubiquitous presence in the embryo. We first demonstrate that mesenchymal-specific loss of PBX1/2 or the transcriptional regulator HAND2 generates similar limb phenotypes. By combining tissue-specific and temporally controlled mutagenesis with multi-omics approaches, we reconstruct a gene regulatory network (GRN) at organismal-level resolution that is collaboratively directed by PBX1/2 and HAND2 interactions in subsets of posterior hindlimb mesenchymal cells. Genome-wide profiling of PBX1 binding across multiple embryonic tissues further reveals that HAND2 interacts with subsets of PBX-bound regions to regulate limb-specific GRNs. Our research elucidates fundamental principles by which promiscuous transcription factors cooperate with cofactors that display domain-restricted localization to instruct tissue-specific developmental programs.
    DOI:  https://doi.org/10.1038/s41467-023-39443-z
  12. Nat Commun. 2023 07 03. 14(1): 3907
    Cancer lineage-specific regulation of YAP responsive elements revealed through large-scale functional epigenomic screens.
    Inês A M Barbosa, Rajaraman Gopalakrishnan, Samuele Mercan, Thanos P Mourikis, Typhaine Martin, Simon Wengert, Caibin Sheng, Fei Ji, Rui Lopes, Judith Knehr, Marc Altorfer, Alicia Lindeman, Carsten Russ, Ulrike Naumann, Javad Golji, Kathleen Sprouffske, Louise Barys, Luca Tordella, Dirk Schübeler, Tobias Schmelzle, Giorgio G Galli.
      YAP is a key transcriptional co-activator of TEADs, it regulates cell growth and is frequently activated in cancer. In Malignant Pleural Mesothelioma (MPM), YAP is activated by loss-of-function mutations in upstream components of the Hippo pathway, while, in Uveal Melanoma (UM), YAP is activated in a Hippo-independent manner. To date, it is unclear if and how the different oncogenic lesions activating YAP impact its oncogenic program, which is particularly relevant for designing selective anti-cancer therapies. Here we show that, despite YAP being essential in both MPM and UM, its interaction with TEAD is unexpectedly dispensable in UM, limiting the applicability of TEAD inhibitors in this cancer type. Systematic functional interrogation of YAP regulatory elements in both cancer types reveals convergent regulation of broad oncogenic drivers in both MPM and UM, but also strikingly selective programs. Our work reveals unanticipated lineage-specific features of the YAP regulatory network that provide important insights to guide the design of tailored therapeutic strategies to inhibit YAP signaling across different cancer types.
    DOI:  https://doi.org/10.1038/s41467-023-39527-w
  13. Nat Cell Biol. 2023 Jul 06.
    Dynamic de novo heterochromatin assembly and disassembly at replication forks ensures fork stability.
    Vincent Gaggioli, Calvin S Y Lo, Nazaret Reverón-Gómez, Zuzana Jasencakova, Heura Domenech, Hong Nguyen, Simone Sidoli, Andrey Tvardovskiy, Sidrit Uruci, Johan A Slotman, Yi Chai, João G S C Souto Gonçalves, Eleni Maria Manolika, Ole N Jensen, David Wheeler, Sriram Sridharan, Sanjiban Chakrabarty, Jeroen Demmers, Roland Kanaar, Anja Groth, Nitika Taneja.
      Chromatin is dynamically reorganized when DNA replication forks are challenged. However, the process of epigenetic reorganization and its implication for fork stability is poorly understood. Here we discover a checkpoint-regulated cascade of chromatin signalling that activates the histone methyltransferase EHMT2/G9a to catalyse heterochromatin assembly at stressed replication forks. Using biochemical and single molecule chromatin fibre approaches, we show that G9a together with SUV39h1 induces chromatin compaction by accumulating the repressive modifications, H3K9me1/me2/me3, in the vicinity of stressed replication forks. This closed conformation is also favoured by the G9a-dependent exclusion of the H3K9-demethylase JMJD1A/KDM3A, which facilitates heterochromatin disassembly upon fork restart. Untimely heterochromatin disassembly from stressed forks by KDM3A enables PRIMPOL access, triggering single-stranded DNA gap formation and sensitizing cells towards chemotherapeutic drugs. These findings may help in explaining chemotherapy resistance and poor prognosis observed in patients with cancer displaying elevated levels of G9a/H3K9me3.
    DOI:  https://doi.org/10.1038/s41556-023-01167-z
  14. PLoS Genet. 2023 Jul 06. 19(7): e1010833
    Characterizing the landscape of gene expression variance in humans.
    Scott Wolf, Diogo Melo, Kristina M Garske, Luisa F Pallares, Amanda J Lea, Julien F Ayroles.
      Gene expression variance has been linked to organismal function and fitness but remains a commonly neglected aspect of molecular research. As a result, we lack a comprehensive understanding of the patterns of transcriptional variance across genes, and how this variance is linked to context-specific gene regulation and gene function. Here, we use 57 large publicly available RNA-seq data sets to investigate the landscape of gene expression variance. These studies cover a wide range of tissues and allowed us to assess if there are consistently more or less variable genes across tissues and data sets and what mechanisms drive these patterns. We show that gene expression variance is broadly similar across tissues and studies, indicating that the pattern of transcriptional variance is consistent. We use this similarity to create both global and within-tissue rankings of variation, which we use to show that function, sequence variation, and gene regulatory signatures contribute to gene expression variance. Low-variance genes are associated with fundamental cell processes and have lower levels of genetic polymorphisms, have higher gene-gene connectivity, and tend to be associated with chromatin states associated with transcription. In contrast, high-variance genes are enriched for genes involved in immune response, environmentally responsive genes, immediate early genes, and are associated with higher levels of polymorphisms. These results show that the pattern of transcriptional variance is not noise. Instead, it is a consistent gene trait that seems to be functionally constrained in human populations. Furthermore, this commonly neglected aspect of molecular phenotypic variation harbors important information to understand complex traits and disease.
    DOI:  https://doi.org/10.1371/journal.pgen.1010833
  15. Nat Commun. 2023 Jul 06. 14(1): 4005
    TET2 and TET3 loss disrupts small intestine differentiation and homeostasis.
    Ihab Ansari, Llorenç Solé-Boldo, Meshi Ridnik, Julian Gutekunst, Oliver Gilliam, Maria Korshko, Timur Liwinski, Birgit Jickeli, Noa Weinberg-Corem, Michal Shoshkes-Carmel, Eli Pikarsky, Eran Elinav, Frank Lyko, Yehudit Bergman.
      TET2/3 play a well-known role in epigenetic regulation and mouse development. However, their function in cellular differentiation and tissue homeostasis remains poorly understood. Here we show that ablation of TET2/3 in intestinal epithelial cells results in a murine phenotype characterized by a severe homeostasis imbalance in the small intestine. Tet2/3-deleted mice show a pronounced loss of mature Paneth cells as well as fewer Tuft and more Enteroendocrine cells. Further results show major changes in DNA methylation at putative enhancers, which are associated with cell fate-determining transcription factors and functional effector genes. Notably, pharmacological inhibition of DNA methylation partially rescues the methylation and cellular defects. TET2/3 loss also alters the microbiome, predisposing the intestine to inflammation under homeostatic conditions and acute inflammation-induced death. Together, our results uncover previously unrecognized critical roles for DNA demethylation, possibly occurring subsequently to chromatin opening during intestinal development, culminating in the establishment of normal intestinal crypts.
    DOI:  https://doi.org/10.1038/s41467-023-39512-3
  16. Sci Adv. 2023 Jul 07. 9(27): eadh2019
    Structural insights into human TFIIIC promoter recognition.
    Wolfram Seifert-Davila, Mathias Girbig, Luis Hauptmann, Thomas Hoffmann, Sebastian Eustermann, Christoph W Müller.
      Transcription factor (TF) IIIC recruits RNA polymerase (Pol) III to most of its target genes. Recognition of intragenic A- and B-box motifs in transfer RNA (tRNA) genes by TFIIIC modules τA and τB is the first critical step for tRNA synthesis but is mechanistically poorly understood. Here, we report cryo-electron microscopy structures of the six-subunit human TFIIIC complex unbound and bound to a tRNA gene. The τB module recognizes the B-box via DNA shape and sequence readout through the assembly of multiple winged-helix domains. TFIIIC220 forms an integral part of both τA and τB connecting the two subcomplexes via a ~550-amino acid residue flexible linker. Our data provide a structural mechanism by which high-affinity B-box recognition anchors TFIIIC to promoter DNA and permits scanning for low-affinity A-boxes and TFIIIB for Pol III activation.
    DOI:  https://doi.org/10.1126/sciadv.adh2019
  17. Nat Biotechnol. 2023 Jul 06.
    De novo detection of somatic mutations in high-throughput single-cell profiling data sets.
    Francesc Muyas, Carolin M Sauer, Jose Espejo Valle-Inclán, Ruoyan Li, Raheleh Rahbari, Thomas J Mitchell, Sahand Hormoz, Isidro Cortés-Ciriano.
      Characterization of somatic mutations at single-cell resolution is essential to study cancer evolution, clonal mosaicism and cell plasticity. Here, we describe SComatic, an algorithm designed for the detection of somatic mutations in single-cell transcriptomic and ATAC-seq (assay for transposase-accessible chromatin sequence) data sets directly without requiring matched bulk or single-cell DNA sequencing data. SComatic distinguishes somatic mutations from polymorphisms, RNA-editing events and artefacts using filters and statistical tests parameterized on non-neoplastic samples. Using >2.6 million single cells from 688 single-cell RNA-seq (scRNA-seq) and single-cell ATAC-seq (scATAC-seq) data sets spanning cancer and non-neoplastic samples, we show that SComatic detects mutations in single cells accurately, even in differentiated cells from polyclonal tissues that are not amenable to mutation detection using existing methods. Validated against matched genome sequencing and scRNA-seq data, SComatic achieves F1 scores between 0.6 and 0.7 across diverse data sets, in comparison to 0.2-0.4 for the second-best performing method. In summary, SComatic permits de novo mutational signature analysis, and the study of clonal heterogeneity and mutational burdens at single-cell resolution.
    DOI:  https://doi.org/10.1038/s41587-023-01863-z
  18. Mol Cell. 2023 Jun 26. pii: S1097-2765(23)00429-X. [Epub ahead of print]
    Oncogenic K-Ras suppresses global miRNA function.
    Bing Shui, Tyler S Beyett, Zhengyi Chen, Xiaoyi Li, Gaspare La Rocca, William M Gazlay, Michael J Eck, Ken S Lau, Andrea Ventura, Kevin M Haigis.
      K-Ras frequently acquires gain-of-function mutations (K-RasG12D being the most common) that trigger significant transcriptomic and proteomic changes to drive tumorigenesis. Nevertheless, oncogenic K-Ras-induced dysregulation of post-transcriptional regulators such as microRNAs (miRNAs) during oncogenesis is poorly understood. Here, we report that K-RasG12D promotes global suppression of miRNA activity, resulting in the upregulation of hundreds of targets. We constructed a comprehensive profile of physiological miRNA targets in mouse colonic epithelium and tumors expressing K-RasG12D using Halo-enhanced Argonaute pull-down. Combining this with parallel datasets of chromatin accessibility, transcriptome, and proteome, we uncovered that K-RasG12D suppressed the expression of Csnk1a1 and Csnk2a1, subsequently decreasing Ago2 phosphorylation at Ser825/829/832/835. Hypo-phosphorylated Ago2 increased binding to mRNAs while reducing its activity to repress miRNA targets. Our findings connect a potent regulatory mechanism of global miRNA activity to K-Ras in a pathophysiological context and provide a mechanistic link between oncogenic K-Ras and the post-transcriptional upregulation of miRNA targets.
    Keywords:  Ago2; CLIP-seq; K-Ras; casein kinase; colon; colorectal cancer; miRNA
    DOI:  https://doi.org/10.1016/j.molcel.2023.06.008
  19. Proc Natl Acad Sci U S A. 2023 02 07. 120(6): e2214824120
    Inducible disruption of Tet genes results in myeloid malignancy, readthrough transcription, and a heterochromatin-to-euchromatin switch.
    Hiroshi Yuita, Isaac F López-Moyado, Hyeongmin Jeong, Arthur Xiuyuan Cheng, James Scott-Browne, Jungeun An, Toshinori Nakayama, Atsushi Onodera, Myunggon Ko, Anjana Rao.
      The three mammalian TET dioxygenases oxidize the methyl group of 5-methylcytosine in DNA, and the oxidized methylcytosines are essential intermediates in all known pathways of DNA demethylation. To define the in vivo consequences of complete TET deficiency, we inducibly deleted all three Tet genes in the mouse genome. Tet1/2/3-inducible TKO (iTKO) mice succumbed to acute myeloid leukemia (AML) by 4 to 5 wk. Single-cell RNA sequencing of Tet iTKO bone marrow cells revealed the appearance of new myeloid cell populations characterized by a striking increase in expression of all members of the stefin/cystatin gene cluster on mouse chromosome 16. In patients with AML, high stefin/cystatin gene expression correlates with poor clinical outcomes. Increased expression of the clustered stefin/cystatin genes was associated with a heterochromatin-to-euchromatin compartment switch with readthrough transcription downstream of the clustered stefin/cystatin genes as well as other highly expressed genes, but only minor changes in DNA methylation. Our data highlight roles for TET enzymes that are distinct from their established function in DNA demethylation and instead involve increased transcriptional readthrough and changes in three-dimensional genome organization.
    Keywords:  Stefins; TET proteins; heterochromatin-to-euchromatin transition; myeloid expansion; readthrough transcription
    DOI:  https://doi.org/10.1073/pnas.2214824120
  20. Nat Commun. 2023 07 04. 14(1): 3946
    Single cohesin molecules generate force by two distinct mechanisms.
    Georgii Pobegalov, Lee-Ya Chu, Jan-Michael Peters, Maxim I Molodtsov.
      Spatial organization of DNA is facilitated by cohesin protein complexes that move on DNA and extrude DNA loops. How cohesin works mechanistically as a molecular machine is poorly understood. Here, we measure mechanical forces generated by conformational changes in single cohesin molecules. We show that bending of SMC coiled coils is driven by random thermal fluctuations leading to a ~32 nm head-hinge displacement that resists forces up to 1 pN; ATPase head engagement occurs in a single step of ~10 nm and is driven by an ATP dependent head-head movement, resisting forces up to 15 pN. Our molecular dynamic simulations show that the energy of head engagement can be stored in a mechanically strained conformation of NIPBL and released during disengagement. These findings reveal how single cohesin molecules generate force by two distinct mechanisms. We present a model, which proposes how this ability may power different aspects of cohesin-DNA interaction.
    DOI:  https://doi.org/10.1038/s41467-023-39696-8
  21. Nucleic Acids Res. 2023 Jul 03. pii: gkad566. [Epub ahead of print]
    Integration of gene expression and DNA methylation data across different experiments.
    Yonatan Itai, Nimrod Rappoport, Ron Shamir.
      Integrative analysis of multi-omic datasets has proven to be extremely valuable in cancer research and precision medicine. However, obtaining multimodal data from the same samples is often difficult. Integrating multiple datasets of different omics remains a challenge, with only a few available algorithms developed to solve it. Here, we present INTEND (IntegratioN of Transcriptomic and EpigeNomic Data), a novel algorithm for integrating gene expression and DNA methylation datasets covering disjoint sets of samples. To enable integration, INTEND learns a predictive model between the two omics by training on multi-omic data measured on the same set of samples. In comprehensive testing on 11 TCGA (The Cancer Genome Atlas) cancer datasets spanning 4329 patients, INTEND achieves significantly superior results compared with four state-of-the-art integration algorithms. We also demonstrate INTEND's ability to uncover connections between DNA methylation and the regulation of gene expression in the joint analysis of two lung adenocarcinoma single-omic datasets from different sources. INTEND's data-driven approach makes it a valuable multi-omic data integration tool. The code for INTEND is available at https://github.com/Shamir-Lab/INTEND.
    DOI:  https://doi.org/10.1093/nar/gkad566
  22. iScience. 2023 Jul 21. 26(7): 107128
    Metabolic regulation of CTCF expression and chromatin association dictates starvation response in mice and flies.
    Devashish Sen, Babukrishna Maniyadath, Shreyam Chowdhury, Arshdeep Kaur, Subhash Khatri, Arnab Chakraborty, Neelay Mehendale, Snigdha Nadagouda, U S Sandra, Siddhesh S Kamat, Ullas Kolthur-Seetharam.
      Coordinated temporal control of gene expression is essential for physiological homeostasis, especially during metabolic transitions. However, the interplay between chromatin architectural proteins and metabolism in regulating transcription is less understood. Here, we demonstrate a conserved bidirectional interplay between CTCF (CCCTC-binding factor) expression/function and metabolic inputs during feed-fast cycles. Our results indicate that its loci-specific functional diversity is associated with physiological plasticity in mouse hepatocytes. CTCF differential expression and long non-coding RNA-Jpx mediated changes in chromatin occupancy, unraveled its paradoxical yet tuneable functions, which are governed by metabolic inputs. We illustrate the key role of CTCF in controlling temporal cascade of transcriptional response, with effects on hepatic mitochondrial energetics and lipidome. Underscoring the evolutionary conservation of CTCF-dependent metabolic homeostasis, CTCF knockdown in flies abrogated starvation resistance. In summary, we demonstrate the interplay between CTCF and metabolic inputs that highlights the coupled plasticity of physiological responses and chromatin function.
    Keywords:  Biological sciences; Natural sciences
    DOI:  https://doi.org/10.1016/j.isci.2023.107128
  23. Cell Rep. 2023 Jul 04. pii: S2211-1247(23)00750-7. [Epub ahead of print]42(7): 112739
    Sugar-responsive inhibition of Myc-dependent ribosome biogenesis by Clockwork orange.
    Linda van den Berg, Krista Kokki, Sylvia J Wowro, Konstantin M Petricek, Onur Deniz, Catrin A Stegmann, Marius Robciuc, Mari Teesalu, Richard G Melvin, Anni I Nieminen, Michael Schupp, Ville Hietakangas.
      The ability to feed on a sugar-containing diet depends on a gene regulatory network controlled by the intracellular sugar sensor Mondo/ChREBP-Mlx, which remains insufficiently characterized. Here, we present a genome-wide temporal clustering of sugar-responsive gene expression in Drosophila larvae. We identify gene expression programs responding to sugar feeding, including downregulation of ribosome biogenesis genes, known targets of Myc. Clockwork orange (CWO), a component of the circadian clock, is found to be a mediator of this repressive response and to be necessary for survival on a high-sugar diet. CWO expression is directly activated by Mondo-Mlx, and it counteracts Myc through repression of its gene expression and through binding to overlapping genomic regions. CWO mouse ortholog BHLHE41 has a conserved role in repressing ribosome biogenesis genes in primary hepatocytes. Collectively, our data uncover a cross-talk between conserved gene regulatory circuits balancing the activities of anabolic pathways to maintain homeostasis during sugar feeding.
    Keywords:  CP: Molecular biology; Drosophila; hepatocyte; metabolism; nutrient sensing; ribosome biogenesis; sugar; transcription
    DOI:  https://doi.org/10.1016/j.celrep.2023.112739
  24. iScience. 2023 Jul 21. 26(7): 107115
    An EZH2-NF-κB regulatory axis drives expression of pro-oncogenic gene signatures in triple negative breast cancer.
    Gabrielle J Dardis, Jun Wang, Jeremy M Simon, Gang Greg Wang, Albert S Baldwin.
      The histone methyltransferase EZH2 has been studied most extensively in the context of PRC2-dependent gene repression. Accumulating evidence indicates non-canonical functions for EZH2 in cancer contexts including promoting paradoxical gene expression through interactions with transcription factors, including NF-κB in triple negative breast cancer (TNBC). We profile EZH2 and NF-κB factor co-localization and positive gene regulation genome-wide, and define a subset of NF-κB targets and genes associated with oncogenic functions in TNBC that is enriched in patient datasets. We demonstrate interaction between EZH2 and RelA requiring the recently identified transactivation domain (TAD) which mediates EZH2 recruitment to, and activation of certain NF-κB-dependent genes, and supports downstream migration and stemness phenotypes in TNBC cells. Interestingly, EZH2-NF-κB positive regulation of genes and stemness does not require PRC2. This study provides new insight into pro-oncogenic regulatory functions for EZH2 in breast cancer through PRC2-independent, and NF-κB-dependent regulatory mechanisms.
    Keywords:  Biochemistry; Biological sciences; Cancer; Cancer systems biology; Natural sciences; Systems biology
    DOI:  https://doi.org/10.1016/j.isci.2023.107115
  25. Genome Biol Evol. 2023 Jul 06. pii: evad126. [Epub ahead of print]
    Cis-regulatory landscape size, constraint, and tissue-specificity associate with gene function and expression.
    Mary Lauren Benton, Douglas M Ruderfer, John A Capra.
      Multiple distal cis-regulatory elements (CREs) often cooperate to regulate gene expression, and the presence of multiple CREs for a gene has been proposed to provide redundancy and robustness to variation. However, we do not understand how attributes of a gene's distal CRE landscape-the CREs that contribute to its regulation-relate to its expression and function. Here, we integrate three-dimensional chromatin conformation and functional genomics data to quantify the CRE landscape composition genome-wide across ten human tissues and relate their attributes to the function, constraint, and expression patterns of genes. Within each tissue, we find that expressed genes have larger CRE landscapes than non-expressed genes and that genes with tissue-specific CREs are more likely to have tissue-specific expression. Controlling for the association between expression level and CRE landscape size, we also find that CRE landscapes around genes under strong constraint (e.g., loss-of-function intolerant and housekeeping genes) are not significantly smaller than other expressed genes as previously proposed; however, they do have more evolutionarily conserved sequences than CREs of expressed genes overall. We also show that CRE landscape size does not associate with expression variability across individuals; nonetheless, genes with larger CRE landscapes have a relative depletion for variants that influence expression levels (eQTL). Overall, this work illustrates how differences in gene function, expression, and evolutionary constraint are reflected in features of CRE landscapes. Thus, considering the CRE landscape of a gene is vital for understanding gene expression dynamics across biological contexts and interpreting the effects of non-coding genetic variants.
    Keywords:  cis-regulatory element; gene regulation; regulatory landscape; tissue-specific gene expression
    DOI:  https://doi.org/10.1093/gbe/evad126
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