bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2022–11–27
eightteen papers selected by
Connor Rogerson, University of Cambridge
  1. EBF1 is continuously required for stabilizing local chromatin accessibility in pro-B cells.
  2. Profiling Accessible Chromatin and Nucleosomes in the Mammalian Genome.
  3. Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation.
  4. XLID syndrome gene Med12 promotes Ig isotype switching through chromatin modification and enhancer RNA regulation.
  5. Integration of 3D genome topology and local chromatin features uncovers enhancers underlying craniofacial-specific cartilage defects.
  6. CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells.
  7. De novo methylation of histone H3K23 by the methyltransferases EHMT1/GLP and EHMT2/G9a.
  8. Primate-specific transposable elements shape transcriptional networks during human development.
  9. Differential phosphorylation of Clr4SUV39H by Cdk1 accompanies a histone H3 methylation switch that is essential for gametogenesis.
  10. SOX9 and TCF transcription factors associate to mediate Wnt/β-catenin target gene activation in colorectal cancer.
  11. Identification of genomic binding sites and direct target genes for the transcription factor DDIT3/CHOP.
  12. PPARγ lipodystrophy mutants reveal intermolecular interactions required for enhancer activation.
  13. Structures of transcription preinitiation complex engaged with the +1 nucleosome.
  14. Integrating transcription factor occupancy with transcriptome-wide association analysis identifies susceptibility genes in human cancers.
  15. Oct4:Sox2 binding is essential for establishing but not maintaining active and silent states of dynamically regulated genes in pluripotent cells.
  16. MYC multimers shield stalled replication forks from RNA polymerase.
  17. Zygotic genome activation by the totipotency pioneer factor Nr5a2.
  18. PICH acts as a force-dependent nucleosome remodeler.
  1. Proc Natl Acad Sci U S A. 2022 Nov 29. 119(48): e2210595119
    EBF1 is continuously required for stabilizing local chromatin accessibility in pro-B cells.
    Nikolay Zolotarev, Marc Bayer, Rudolf Grosschedl.
      The establishment of de novo chromatin accessibility in lymphoid progenitors requires the "pioneering" function of transcription factor (TF) early B cell factor 1 (EBF1), which binds to naïve chromatin and induces accessibility by recruiting the BRG1 chromatin remodeler subunit. However, it remains unclear whether the function of EBF1 is continuously required for stabilizing local chromatin accessibility. To this end, we replaced EBF1 by EBF1-FKBPF36V in pro-B cells, allowing the rapid degradation by adding the degradation TAG13 (dTAG13) dimerizer. EBF1 degradation results in a loss of genome-wide EBF1 occupancy and EBF1-targeted BRG1 binding. Chromatin accessibility was rapidly diminished at EBF1-binding sites with a preference for sites whose occupancy requires the pioneering activity of the C-terminal domain of EBF1. Diminished chromatin accessibility correlated with altered gene expression. Thus, continuous activity of EBF1 is required for the stable maintenance of the transcriptional and epigenetic state of pro-B cells.
    Keywords:  B cell; BRG1; EBF1; chromatin accessibility; dTAG
    DOI:  https://doi.org/10.1073/pnas.2210595119
  2. Methods Mol Biol. 2023 ;2599 59-68
    Profiling Accessible Chromatin and Nucleosomes in the Mammalian Genome.
    Hee-Woong Lim, Makiko Iwafuchi.
      Genomic DNA wraps around core histones to form nucleosomes, which provides steric constraints on how transcription factors (TFs) can interact with gene regulatory sequences. It is increasingly apparent that well-positioned, accessible nucleosomes are an inherent feature of active enhancers and can facilitate cooperative TF binding, referred to as nucleosome-mediated cooperativity. Thus, profiling chromatin and nucleosome properties (accessibility, positioning, and occupancy) on the genome is crucial to understand cell-type-specific gene regulation. Here we describe a simplified protocol to profile accessible nucleosomes in the mammalian genome using low-level and high-level micrococcal nuclease (MNase) digestion followed by genome-wide sequencing.
    Keywords:  Accessible nucleosome; Chromatin accessibility; Fragile nucleosome; MNase-seq; Nucleosome occupancy; Nucleosome positioning
    DOI:  https://doi.org/10.1007/978-1-0716-2847-8_6
  3. Mol Cell. 2022 Nov 17. pii: S1097-2765(22)01064-4. [Epub ahead of print]
    Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation.
    Justyna A Janas, Lichao Zhang, Jacklyn H Luu, Janos Demeter, Lingjun Meng, Samuele G Marro, Moritz Mall, Nancie A Mooney, Katie Schaukowitch, Yi Han Ng, Nan Yang, Yuhao Huang, Gernot Neumayer, Or Gozani, Joshua E Elias, Peter K Jackson, Marius Wernig.
      Cell lineage specification is accomplished by a concerted action of chromatin remodeling and tissue-specific transcription factors. However, the mechanisms that induce and maintain appropriate lineage-specific gene expression remain elusive. Here, we used an unbiased proteomics approach to characterize chromatin regulators that mediate the induction of neuronal cell fate. We found that Tip60 acetyltransferase is essential to establish neuronal cell identity partly via acetylation of the histone variant H2A.Z. Despite its tight correlation with gene expression and active chromatin, loss of H2A.Z acetylation had little effect on chromatin accessibility or transcription. Instead, loss of Tip60 and acetyl-H2A.Z interfered with H3K4me3 deposition and activation of a unique subset of silent, lineage-restricted genes characterized by a bivalent chromatin configuration at their promoters. Altogether, our results illuminate the mechanisms underlying bivalent chromatin activation and reveal that H2A.Z acetylation regulates neuronal fate specification by establishing epigenetic competence for bivalent gene activation and cell lineage transition.
    Keywords:  Ascl1; H2A.Z acetylation; H3K4me3; Tip60/Kat5; bivalent chromatin; cell fate; gene activation; neurogenesis; reprogramming; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2022.11.002
  4. Sci Adv. 2022 Nov 25. 8(47): eadd1466
    XLID syndrome gene Med12 promotes Ig isotype switching through chromatin modification and enhancer RNA regulation.
    Farazul Haque, Tasuku Honjo, Nasim A Begum.
      The transcriptional coactivator Med12 regulates gene expression through its kinase module. Here, we show a kinase module-independent function of Med12 in CSR. Med12 is essential for super-enhancer activation by collaborating with p300-Jmjd6/Carm1 coactivator complexes. Med12 loss decreases H3K27 acetylation and eRNA transcription with concomitant impairment of AID-induced DNA breaks, S-S synapse formation, and 3'RR-Eμ interaction. CRISPR-dCas9-mediated enhancer activation reestablishes the epigenomic and transcriptional hallmarks of the super-enhancer and fully restores the Med12 depletion defects. Moreover, 3'RR-derived eRNAs are critical for promoting S region epigenetic regulation, synapse formation, and recruitment of Med12 and AID to the IgH locus. We find that XLID syndrome-associated Med12 mutations are defective in both 3'RR eRNA transcription and CSR, suggesting that B and neuronal cells may have cell-specific super-enhancer dysfunctions. We conclude that Med12 is essential for IgH 3'RR activation/eRNA transcription and plays a central role in AID-induced antibody gene diversification and genomic instability in B cells.
    DOI:  https://doi.org/10.1126/sciadv.add1466
  5. Sci Adv. 2022 Nov 25. 8(47): eabo3648
    Integration of 3D genome topology and local chromatin features uncovers enhancers underlying craniofacial-specific cartilage defects.
    Qiming Chen, Jiewen Dai, Qian Bian.
      Aberrations in tissue-specific enhancers underlie many developmental defects. Disrupting a noncoding region distal from the human SOX9 gene causes the Pierre Robin sequence (PRS) characterized by the undersized lower jaw. Such a craniofacial-specific defect has been previously linked to enhancers transiently active in cranial neural crest cells (CNCCs). We demonstrate that the PRS region also strongly regulates Sox9 in CNCC-derived Meckel's cartilage (MC), but not in limb cartilages, even after decommissioning of CNCC enhancers. Such an MC-specific regulatory effect correlates with the MC-specific chromatin contacts between the PRS region and Sox9, highlighting the importance of lineage-dependent chromatin topology in instructing enhancer usage. By integrating the enhancer signatures and chromatin topology, we uncovered >10,000 enhancers that function differentially between MC and limb cartilages and demonstrated their association with human diseases. Our findings provide critical insights for understanding the choreography of gene regulation during development and interpreting the genetic basis of craniofacial pathologies.
    DOI:  https://doi.org/10.1126/sciadv.abo3648
  6. Nucleic Acids Res. 2022 Nov 21. pii: gkac1090. [Epub ahead of print]
    CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells.
    Dongyu Zhao, Min Zhang, Shaodong Huang, Qi Liu, Sen Zhu, Yanqiang Li, Weihua Jiang, Daniel L Kiss, Qi Cao, Lili Zhang, Kaifu Chen.
      Despite being a member of the chromodomain helicase DNA-binding protein family, little is known about the exact role of CHD6 in chromatin remodeling or cancer disease. Here we show that CHD6 binds to chromatin to promote broad nucleosome eviction for transcriptional activation of many cancer pathways. By integrating multiple patient cohorts for bioinformatics analysis of over a thousand prostate cancer datasets, we found CHD6 expression elevated in prostate cancer and associated with poor prognosis. Further comprehensive experiments demonstrated that CHD6 regulates oncogenicity of prostate cancer cells and tumor development in a murine xenograft model. ChIP-Seq for CHD6, along with MNase-Seq and RNA-Seq, revealed that CHD6 binds on chromatin to evict nucleosomes from promoters and gene bodies for transcriptional activation of oncogenic pathways. These results demonstrated a key function of CHD6 in evicting nucleosomes from chromatin for transcriptional activation of prostate cancer pathways.
    DOI:  https://doi.org/10.1093/nar/gkac1090
  7. Epigenetics Chromatin. 2022 Nov 21. 15(1): 36
    De novo methylation of histone H3K23 by the methyltransferases EHMT1/GLP and EHMT2/G9a.
    David A Vinson, Kimberly E Stephens, Robert N O'Meally, Shri Bhat, Blair C R Dancy, Robert N Cole, Srinivasan Yegnasubramanian, Sean D Taverna.
      Epigenetic modifications to histone proteins serve an important role in regulating permissive and repressive chromatin states, but despite the identification of many histone PTMs and their perceived role, the epigenetic writers responsible for generating these chromatin signatures are not fully characterized. Here, we report that the canonical histone H3K9 methyltransferases EHMT1/GLP and EHMT2/G9a are capable of catalyzing methylation of histone H3 lysine 23 (H3K23). Our data show that while both enzymes can mono- and di-methylate H3K23, only EHMT1/GLP can tri-methylate H3K23. We also show that pharmacologic inhibition or genetic ablation of EHMT1/GLP and/or EHMT2/G9a leads to decreased H3K23 methylation in mammalian cells. Taken together, this work identifies H3K23 as a new direct methylation target of EHMT1/GLP and EHMT2/G9a, and highlights the differential activity of these enzymes on H3K23 as a substrate.
    Keywords:  EHMT1; EHMT2; Epigenetics; G9a; GLP; H3K18 methylation; H3K23 methylation; Histone
    DOI:  https://doi.org/10.1186/s13072-022-00468-1
  8. Nat Commun. 2022 Nov 23. 13(1): 7178
    Primate-specific transposable elements shape transcriptional networks during human development.
    Julien Pontis, Cyril Pulver, Christopher J Playfoot, Evarist Planet, Delphine Grun, Sandra Offner, Julien Duc, Andrea Manfrin, Matthias P Lutolf, Didier Trono.
      The human genome contains more than 4.5 million inserts derived from transposable elements (TEs), the result of recurrent waves of invasion and internal propagation throughout evolution. For new TE copies to be inherited, they must become integrated in the genome of the germline or pre-implantation embryo, which requires that their source TE be expressed at these stages. Accordingly, many TEs harbor DNA binding sites for the pluripotency factors OCT4, NANOG, SOX2, and KLFs and are transiently expressed during embryonic genome activation. Here, we describe how many primate-restricted TEs have additional binding sites for lineage-specific transcription factors driving their expression during human gastrulation and later steps of fetal development. These TE integrants serve as lineage-specific enhancers fostering the transcription, amongst other targets, of KRAB-zinc finger proteins (KZFPs) of comparable evolutionary age, which in turn corral the activity of TE-embedded regulatory sequences in a similarly lineage-restricted fashion. Thus, TEs and their KZFP controllers play broad roles in shaping transcriptional networks during early human development.
    DOI:  https://doi.org/10.1038/s41467-022-34800-w
  9. EMBO Rep. 2022 Nov 21. e55928
    Differential phosphorylation of Clr4SUV39H by Cdk1 accompanies a histone H3 methylation switch that is essential for gametogenesis.
    Tahsin Kuzdere, Valentin Flury, Thomas Schalch, Vytautas Iesmantavicius, Daniel Hess, Marc Bühler.
      Methylation of histone H3 at lysine 9 (H3K9) is a hallmark of heterochromatin that plays crucial roles in gene silencing, genome stability, and chromosome segregation. In Schizosaccharomyces pombe, Clr4 mediates both di- and tri-methylation of H3K9. Although H3K9 methylation has been intensely studied in mitotic cells, its role during sexual differentiation remains unclear. Here, we map H3K9 methylation genome-wide during meiosis and show that constitutive heterochromatin temporarily loses H3K9me2 and becomes H3K9me3 when cells commit to meiosis. Cells lacking the ability to tri-methylate H3K9 exhibit meiotic chromosome segregation defects. Finally, the H3K9 methylation switch is accompanied by differential phosphorylation of Clr4 by the cyclin-dependent kinase Cdk1. Our results suggest that a conserved master regulator of the cell cycle controls the specificity of an H3K9 methyltransferase to prevent ectopic H3K9 methylation and to ensure faithful gametogenesis.
    Keywords:  chromosome segregation; fission yeast; histone methylation; meiosis; phosphorylation
    DOI:  https://doi.org/10.15252/embr.202255928
  10. J Biol Chem. 2022 Nov 21. pii: S0021-9258(22)01178-4. [Epub ahead of print] 102735
    SOX9 and TCF transcription factors associate to mediate Wnt/β-catenin target gene activation in colorectal cancer.
    Aravinda-Bharathi Ramakrishnan, Peter E Burby, Kavya Adiga, Ken M Cadigan.
      Activation of the Wnt/β-catenin pathway regulates gene expression by promoting the formation of a β-catenin-T cell factor (TCF) complex on target enhancers. In addition to TCFs, other transcription factors interact with the Wnt/β-catenin pathway at different levels to produce tissue-specific patterns of Wnt target gene expression. The transcription factor SOX9 potently represses many Wnt target genes by down-regulating β-catenin protein levels. Here, we find using colony formation and cell growth assays that SOX9 surprisingly promotes the proliferation of Wnt-driven colorectal cancer (CRC) cells. In contrast to how it indirectly represses Wnt targets, SOX9 directly co-occupies and activates multiple Wnt-responsive enhancers in CRC cells. Our examination of the binding site grammar of these enhancers shows the presence of TCF and SOX9 binding sites that are necessary for transcriptional activation. In addition, we identify a physical interaction between the DNA-binding domains of TCFs and SOX9 and show that TCF-SOX9 interactions are important for target gene regulation and CRC cell growth. Our work demonstrates a highly context-dependent effect of SOX9 on Wnt targets, with the presence or absence of SOX9 binding sites on Wnt-regulated enhancers determining whether they are directly activated or indirectly repressed by SOX9.
    Keywords:  Wnt pathway; Wnt signaling; colorectal cancer; enhancers; gene transcription; transcription factor
    DOI:  https://doi.org/10.1016/j.jbc.2022.102735
  11. Exp Cell Res. 2022 Nov 17. pii: S0014-4827(22)00411-6. [Epub ahead of print]422(1): 113418
    Identification of genomic binding sites and direct target genes for the transcription factor DDIT3/CHOP.
    Ayman Osman, Malin Lindén, Tobias Österlund, Christoffer Vannas, Lisa Andersson, Mandy Escobar, Anders Ståhlberg, Pierre Åman.
      DDIT3 is a tightly regulated basic leucine zipper (bZIP) transcription factor and key regulator in cellular stress responses. It is involved in a variety of pathological conditions and may cause cell cycle block and apoptosis. It is also implicated in differentiation of some specialized cell types and as an oncogene in several types of cancer. DDIT3 was originally believed to act as a dominant-negative inhibitor by forming heterodimers with other bZIP transcription factors, preventing their DNA binding and transactivating functions. DDIT3 has, however, been reported to bind DNA and regulate target genes. Here, we employed ChIP sequencing combined with microarray-based expression analysis to identify direct binding motifs and target genes of DDIT3. The results reveal DDIT3 binding to motifs similar to other bZIP transcription factors, known to form heterodimers with DDIT3. Binding to a class III satellite DNA repeat sequence was also detected. DDIT3 acted as a DNA-binding transcription factor and bound mainly to the promotor region of regulated genes. ChIP sequencing analysis of histone H3K27 methylation and acetylation showed a strong overlap between H3K27-acetylated marks and DDIT3 binding. These results support a role for DDIT3 as a transcriptional regulator of H3K27ac-marked genes in transcriptionally active chromatin.
    Keywords:  CHOP; ChIP-seq; DDIT3; Gene function; Transcriptional regulation; bZIP transcription factor
    DOI:  https://doi.org/10.1016/j.yexcr.2022.113418
  12. Nat Commun. 2022 Nov 19. 13(1): 7090
    PPARγ lipodystrophy mutants reveal intermolecular interactions required for enhancer activation.
    Maria Stahl Madsen, Marjoleine F Broekema, Martin Rønn Madsen, Arjen Koppen, Anouska Borgman, Cathrin Gräwe, Elisabeth G K Thomsen, Denise Westland, Mariette E G Kranendonk, Marian Groot Koerkamp, Nicole Hamers, Alexandre M J J Bonvin, José M Ramos Pittol, Kedar Nath Natarajan, Sander Kersten, Frank C P Holstege, Houshang Monajemi, Saskia W C van Mil, Michiel Vermeulen, Birthe B Kragelund, David Cassiman, Susanne Mandrup, Eric Kalkhoven.
      Peroxisome proliferator-activated receptor γ (PPARγ) is the master regulator of adipocyte differentiation, and mutations that interfere with its function cause lipodystrophy. PPARγ is a highly modular protein, and structural studies indicate that PPARγ domains engage in several intra- and inter-molecular interactions. How these interactions modulate PPARγ's ability to activate target genes in a cellular context is currently poorly understood. Here we take advantage of two previously uncharacterized lipodystrophy mutations, R212Q and E379K, that are predicted to interfere with the interaction of the hinge of PPARγ with DNA and with the interaction of PPARγ ligand binding domain (LBD) with the DNA-binding domain (DBD) of the retinoid X receptor, respectively. Using biochemical and genome-wide approaches we show that these mutations impair PPARγ function on an overlapping subset of target enhancers. The hinge region-DNA interaction appears mostly important for binding and remodelling of target enhancers in inaccessible chromatin, whereas the PPARγ-LBD:RXR-DBD interface stabilizes the PPARγ:RXR:DNA ternary complex. Our data demonstrate how in-depth analyses of lipodystrophy mutants can unravel molecular mechanisms of PPARγ function.
    DOI:  https://doi.org/10.1038/s41467-022-34766-9
  13. Nat Struct Mol Biol. 2022 Nov 21.
    Structures of transcription preinitiation complex engaged with the +1 nucleosome.
    Haibo Wang, Sandra Schilbach, Momchil Ninov, Henning Urlaub, Patrick Cramer.
      The preinitiation complex (PIC) assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation. Previous structural studies revealed the PIC on different promoters, but did not address how the PIC assembles within chromatin. In the yeast Saccharomyces cerevisiae, PIC assembly occurs adjacent to the +1 nucleosome that is located downstream of the core promoter. Here we present cryo-EM structures of the yeast PIC bound to promoter DNA and the +1 nucleosome located at three different positions. The general transcription factor TFIIH engages with the incoming downstream nucleosome and its translocase subunit Ssl2 (XPB in human TFIIH) drives the rotation of the +1 nucleosome leading to partial detachment of nucleosomal DNA and intimate interactions between TFIIH and the nucleosome. The structures provide insights into how transcription initiation can be influenced by the +1 nucleosome and may explain why the transcription start site is often located roughly 60 base pairs upstream of the dyad of the +1 nucleosome in yeast.
    DOI:  https://doi.org/10.1038/s41594-022-00865-w
  14. Nat Commun. 2022 Nov 19. 13(1): 7118
    Integrating transcription factor occupancy with transcriptome-wide association analysis identifies susceptibility genes in human cancers.
    Jingni He, Wanqing Wen, Alicia Beeghly, Zhishan Chen, Chen Cao, Xiao-Ou Shu, Wei Zheng, Quan Long, Xingyi Guo.
      Transcriptome-wide association studies (TWAS) have successfully discovered many putative disease susceptibility genes. However, TWAS may suffer from inaccuracy of gene expression predictions due to inclusion of non-regulatory variants. By integrating prior knowledge of susceptible transcription factor occupied elements, we develop sTF-TWAS and demonstrate that it outperforms existing TWAS approaches in both simulation and real data analyses. Under the sTF-TWAS framework, we build genetic models to predict alternative splicing and gene expression in normal breast, prostate and lung tissues from the Genotype-Tissue Expression project and apply these models to data from large genome-wide association studies (GWAS) conducted among European-ancestry populations. At Bonferroni-corrected P < 0.05, we identify 354 putative susceptibility genes for these cancers, including 189 previously unreported in GWAS loci and 45 in loci unreported by GWAS. These findings provide additional insight into the genetic susceptibility of human cancers. Additionally, we show the generalizability of the sTF-TWAS on non-cancer diseases.
    DOI:  https://doi.org/10.1038/s41467-022-34888-0
  15. Genes Dev. 2022 Nov 23.
    Oct4:Sox2 binding is essential for establishing but not maintaining active and silent states of dynamically regulated genes in pluripotent cells.
    Jerry Hung-Hao Lo, Miguel Edwards, Justin Langerman, Rupa Sridharan, Kathrin Plath, Stephen T Smale.
      Much has been learned about the mechanisms of action of pluripotency factors Oct4 and Sox2. However, as with other regulators of cell identity, little is known about the impact of disrupting their binding motifs in a native environment or the characteristics of genes they regulate. By quantitatively examining dynamic ranges of gene expression instead of focusing on conventional measures of differential expression, we found that Oct4 and Sox2 enhancer binding is strongly enriched near genes subject to large dynamic ranges of expression among cell types, with binding sites near these genes usually within superenhancers. Mutagenesis of representative Oct4:Sox2 motifs near such active, dynamically regulated genes revealed critical roles in transcriptional activation during reprogramming, with more limited roles in transcriptional maintenance in the pluripotent state. Furthermore, representative motifs near silent genes were critical for establishing but not maintaining the fully silent state, while genes whose transcript levels varied by smaller magnitudes among cell types were unaffected by nearby Oct4:Sox2 motifs. These results suggest that Oct4 and Sox2 directly establish both active and silent transcriptional states in pluripotent cells at a large number of genes subject to dynamic regulation during mammalian development, but are less important than expected for maintaining transcriptional states.
    Keywords:  Oct4; Sox2; differentiation; embryonic stem cells; pluripotency; transcription
    DOI:  https://doi.org/10.1101/gad.350113.122
  16. Nature. 2022 Nov 23.
    MYC multimers shield stalled replication forks from RNA polymerase.
    Daniel Solvie, Apoorva Baluapuri, Leonie Uhl, Daniel Fleischhauer, Theresa Endres, Dimitrios Papadopoulos, Amel Aziba, Abdallah Gaballa, Ivan Mikicic, Ekaterina Isaakova, Celeste Giansanti, Jennifer Jansen, Marvin Jungblut, Teresa Klein, Christina Schülein-Völk, Hans Maric, Sören Doose, Markus Sauer, Petra Beli, Andreas Rosenwald, Matthias Dobbelstein, Elmar Wolf, Martin Eilers.
      Oncoproteins of the MYC family drive the development of numerous human tumours1. In unperturbed cells, MYC proteins bind to nearly all active promoters and control transcription by RNA polymerase II2,3. MYC proteins can also coordinate transcription with DNA replication4,5 and promote the repair of transcription-associated DNA damage6, but how they exert these mechanistically diverse functions is unknown. Here we show that MYC dissociates from many of its binding sites in active promoters and forms multimeric, often sphere-like structures in response to perturbation of transcription elongation, mRNA splicing or inhibition of the proteasome. Multimerization is accompanied by a global change in the MYC interactome towards proteins involved in transcription termination and RNA processing. MYC multimers accumulate on chromatin immediately adjacent to stalled replication forks and surround FANCD2, ATR and BRCA1 proteins, which are located at stalled forks7,8. MYC multimerization is triggered in a HUWE16 and ubiquitylation-dependent manner. At active promoters, MYC multimers block antisense transcription and stabilize FANCD2 association with chromatin. This limits DNA double strand break formation during S-phase, suggesting that the multimerization of MYC enables tumour cells to proliferate under stressful conditions.
    DOI:  https://doi.org/10.1038/s41586-022-05469-4
  17. Science. 2022 Nov 24. eabn7478
    Zygotic genome activation by the totipotency pioneer factor Nr5a2.
    Johanna Gassler, Wataru Kobayashi, Imre Gáspár, Siwat Ruangroengkulrith, Adarsh Mohanan, Laura Gómez Hernández, Pavel Kravchenko, Maximilian Kümmecke, Aleksandar Lalic, Nikita Rifel, Robert John Ashburn, Maciej Zaczek, Antoine Vallot, Laura Cuenca Rico, Sabrina Ladstätter, Kikuë Tachibana.
      Life begins with a switch in genetic control from the maternal to the embryonic genome during zygotic genome activation (ZGA). Despite its importance, the essential regulators of ZGA remain largely unknown in mammals. Based on de novo motif searches, we identified the orphan nuclear receptor Nr5a2 as a key activator of major ZGA in mouse 2-cell embryos. Nr5a2 is required for progression beyond the 2-cell stage. It binds to its motif within SINE B1/Alu retrotransposable elements found in cis-regulatory regions of ZGA genes. Chemical inhibition suggests that 72% of ZGA genes are regulated by Nr5a2 and potentially other orphan nuclear receptors. Nr5a2 promotes chromatin accessibility during ZGA and binds nucleosomal DNA in vitro. We conclude that Nr5a2 is an essential pioneer factor that regulates ZGA.
    DOI:  https://doi.org/10.1126/science.abn7478
  18. Nat Commun. 2022 Nov 25. 13(1): 7277
    PICH acts as a force-dependent nucleosome remodeler.
    Dian Spakman, Tinka V M Clement, Andreas S Biebricher, Graeme A King, Manika I Singh, Ian D Hickson, Erwin J G Peterman, Gijs J L Wuite.
      In anaphase, any unresolved DNA entanglements between the segregating sister chromatids can give rise to chromatin bridges. To prevent genome instability, chromatin bridges must be resolved prior to cytokinesis. The SNF2 protein PICH has been proposed to play a direct role in this process through the remodeling of nucleosomes. However, direct evidence of nucleosome remodeling by PICH has remained elusive. Here, we present an in vitro single-molecule assay that mimics chromatin under tension, as is found in anaphase chromatin bridges. Applying a combination of dual-trap optical tweezers and fluorescence imaging of PICH and histones bound to a nucleosome-array construct, we show that PICH is a tension- and ATP-dependent nucleosome remodeler that facilitates nucleosome unwrapping and then subsequently slides remaining histones along the DNA. This work elucidates the role of PICH in chromatin-bridge dissolution, and might provide molecular insights into the mechanisms of related SNF2 proteins.
    DOI:  https://doi.org/10.1038/s41467-022-35040-8
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