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Dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm

Author

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  • Zeyang Wang

    (Biomedical Center, Faculty of Medicine, LMU Munich)

  • Rui Fan

    (Biomedical Center, Faculty of Medicine, LMU Munich
    Max Planck Institute for Molecular Biomedicine)

  • Angela Russo

    (Biomedical Center, Faculty of Medicine, LMU Munich)

  • Filippo M. Cernilogar

    (Biomedical Center, Faculty of Medicine, LMU Munich)

  • Alexander Nuber

    (Biomedical Center, Faculty of Medicine, LMU Munich)

  • Silvia Schirge

    (Institute of Stem Cell Research
    Institute of Diabetes and Regeneration Research)

  • Irina Shcherbakova

    (Biomedical Center, Faculty of Medicine, LMU Munich)

  • Iva Dzhilyanova

    (Biomedical Center, Faculty of Medicine, LMU Munich)

  • Enes Ugur

    (Biozentrum, LMU Munich)

  • Tobias Anton

    (Biozentrum, LMU Munich)

  • Lisa Richter

    (Core Facility Flow Cytometry, Faculty of Medicine, LMU Munich)

  • Heinrich Leonhardt

    (Biozentrum, LMU Munich)

  • Heiko Lickert

    (Institute of Stem Cell Research
    Institute of Diabetes and Regeneration Research
    German Center for Diabetes Research (DZD)
    Technische Universität München)

  • Gunnar Schotta

    (Biomedical Center, Faculty of Medicine, LMU Munich)

Abstract

Silencing of endogenous retroviruses (ERVs) is largely mediated by repressive chromatin modifications H3K9me3 and DNA methylation. On ERVs, these modifications are mainly deposited by the histone methyltransferase Setdb1 and by the maintenance DNA methyltransferase Dnmt1. Knock-out of either Setdb1 or Dnmt1 leads to ERV de-repression in various cell types. However, it is currently not known if H3K9me3 and DNA methylation depend on each other for ERV silencing. Here we show that conditional knock-out of Setdb1 in mouse embryonic endoderm results in ERV de-repression in visceral endoderm (VE) descendants and does not occur in definitive endoderm (DE). Deletion of Setdb1 in VE progenitors results in loss of H3K9me3 and reduced DNA methylation of Intracisternal A-particle (IAP) elements, consistent with up-regulation of this ERV family. In DE, loss of Setdb1 does not affect H3K9me3 nor DNA methylation, suggesting Setdb1-independent pathways for maintaining these modifications. Importantly, Dnmt1 knock-out results in IAP de-repression in both visceral and definitive endoderm cells, while H3K9me3 is unaltered. Thus, our data suggest a dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm cells. Our findings suggest that Setdb1-meditated H3K9me3 is not sufficient for IAP silencing, but rather critical for maintaining high DNA methylation.

Suggested Citation

  • Zeyang Wang & Rui Fan & Angela Russo & Filippo M. Cernilogar & Alexander Nuber & Silvia Schirge & Irina Shcherbakova & Iva Dzhilyanova & Enes Ugur & Tobias Anton & Lisa Richter & Heinrich Leonhardt & , 2022. "Dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32978-7
    DOI: 10.1038/s41467-022-32978-7
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    References listed on IDEAS

    as
    1. Masaki Kato & Keiko Takemoto & Yoichi Shinkai, 2018. "A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
    2. Sonja Nowotschin & Manu Setty & Ying-Yi Kuo & Vincent Liu & Vidur Garg & Roshan Sharma & Claire S. Simon & Nestor Saiz & Rui Gardner & Stéphane C. Boutet & Deanna M. Church & Pamela A. Hoodless & Anna, 2019. "The emergent landscape of the mouse gut endoderm at single-cell resolution," Nature, Nature, vol. 569(7756), pages 361-367, May.
    3. Qian Zhao & Jiqin Zhang & Ruoyu Chen & Lina Wang & Bo Li & Hao Cheng & Xiaoya Duan & Haijun Zhu & Wei Wei & Jiwen Li & Qihan Wu & Jing-Dong J. Han & Wenqiang Yu & Shaorong Gao & Guohong Li & Jiemin Wo, 2016. "Dissecting the precise role of H3K9 methylation in crosstalk with DNA maintenance methylation in mammals," Nature Communications, Nature, vol. 7(1), pages 1-12, November.
    4. Thomas Wiesner & William Lee & Anna C. Obenauf & Leili Ran & Rajmohan Murali & Qi Fan Zhang & Elissa W. P. Wong & Wenhuo Hu & Sasinya N. Scott & Ronak H. Shah & Iñigo Landa & Julia Button & Nathalie L, 2015. "Alternative transcription initiation leads to expression of a novel ALK isoform in cancer," Nature, Nature, vol. 526(7573), pages 453-457, October.
    5. Xiaoli Liu & Qinqin Gao & Pishun Li & Qian Zhao & Jiqin Zhang & Jiwen Li & Haruhiko Koseki & Jiemin Wong, 2013. "UHRF1 targets DNMT1 for DNA methylation through cooperative binding of hemi-methylated DNA and methylated H3K9," Nature Communications, Nature, vol. 4(1), pages 1-13, June.
    6. Toshiyuki Matsui & Danny Leung & Hiroki Miyashita & Irina A. Maksakova & Hitoshi Miyachi & Hiroshi Kimura & Makoto Tachibana & Matthew C. Lorincz & Yoichi Shinkai, 2010. "Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET," Nature, Nature, vol. 464(7290), pages 927-931, April.
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