The termination of UHRF1-dependent PAF15 ubiquitin signaling is regulated by USP7 and ATAD5

Abstract

UHRF1-dependent ubiquitin signaling plays an integral role in the regulation of maintenance DNA methylation. UHRF1 catalyzes transient dual mono-ubiquitylation of PAF15 (PAF15Ub2), which regulates the localization and activation of DNMT1 at DNA methylation sites during DNA replication. Although the initiation of UHRF1-mediated PAF15 ubiquitin signaling has been relatively well characterized, mechanisms underlying its termination and how they are coordinated with the completion of maintenance DNA methylation have not yet been clarified. This study shows that deubiquitylation by USP7 and unloading by ATAD5 (ELG1 in yeast) are pivotal processes for the removal of PAF15 from chromatin. On replicating chromatin, USP7 specifically interacts with PAF15Ub2 in a complex with DNMT1. USP7 depletion or inhibition of the interaction between USP7 and PAF15 results in abnormal accumulation of PAF15Ub2 on chromatin. Furthermore, we also find that the non-ubiquitylated form of PAF15 (PAF15Ub0) is removed from chromatin in an ATAD5-dependent manner. PAF15Ub2 was retained at high levels on chromatin when the catalytic activity of DNMT1 was inhibited, suggesting that the completion of maintenance DNA methylation is essential for termination of UHRF1-mediated ubiquitin signaling. This finding provides a molecular understanding of how the maintenance DNA methylation machinery is disassembled at the end of the S phase.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files; source data files for all figures have been provided.

Article and author information

Author details

  1. Ryota Miyashita

    Division of Cancer Cell Biology, University of Tokyo, Tokyo, Japan
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1452-8829
  2. Atsuya Nishiyama

    Division of Cancer Cell Biology, University of Tokyo, Tokyo, Japan
    For correspondence
    uanishiyama@g.ecc.u-tokyo.ac.jp
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8416-3776
  3. Weihua Qin

    Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Yoshie Chiba

    Division of Cancer Cell Biology, University of Tokyo, Tokyo, Japan
    Competing interests
    The authors declare that no competing interests exist.
  5. Satomi Kori

    Structural Biology Laboratory, Yokohama City University, Kanagawa, Japan
    Competing interests
    The authors declare that no competing interests exist.
  6. Norie Kato

    Structural Biology Laboratory, Yokohama City University, Kanagawa, Japan
    Competing interests
    The authors declare that no competing interests exist.
  7. Chieko Konishi

    Division of Cancer Cell Biology, University of Tokyo, Tokyo, Japan
    Competing interests
    The authors declare that no competing interests exist.
  8. Soichiro Kumamoto

    Division of Cancer Cell Biology, University of Tokyo, Tokyo, Japan
    Competing interests
    The authors declare that no competing interests exist.
  9. Hiroko Kozuka-Hata

    Institute of Medical Science, University of Tokyo, Tokyo, Japan
    Competing interests
    The authors declare that no competing interests exist.
  10. Masaaki Oyama

    Institute of Medical Science, University of Tokyo, Tokyo, Japan
    Competing interests
    The authors declare that no competing interests exist.
  11. Yoshitaka Kawasoe

    Department of Biology, Kyushu University, Fukuoka, Japan
    Competing interests
    The authors declare that no competing interests exist.
  12. Toshiki Tsurimoto

    Department of Biology, Kyushu University, Fukuoka, Japan
    Competing interests
    The authors declare that no competing interests exist.
  13. Tatsuro S Takahashi

    Department of Biology, Kyushu University, Fukuoka, Japan
    Competing interests
    The authors declare that no competing interests exist.
  14. Heinrich Leonhardt

    Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
  15. Kyohei Arita

    Structural Biology Laboratory, Yokohama City University, Kanagawa, Japan
    Competing interests
    The authors declare that no competing interests exist.
  16. Makoto Nakanishi

    Division of Cancer Cell Biology, University of Tokyo, Tokyo, Japan
    For correspondence
    mkt-naka@g.ecc.u-tokyo.ac.jp
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6707-3584

Funding

MEXT/JSPS (JP19H05740)

  • Makoto Nakanishi

MEXT/JSPS (JP19H03143)

  • Atsuya Nishiyama

MEXT/JSPS (JP19H05285)

  • Atsuya Nishiyama

MEXT/JSPS (JP16H06578)

  • Masaaki Oyama

MEXT/JSPS (JP19H05741)

  • Kyohei Arita

MEXT/JSPS (20H03186)

  • Tatsuro S Takahashi

MEXT/JSPS (20H05392)

  • Tatsuro S Takahashi

MEXT/JSPS (19K16042)

  • Yoshitaka Kawasoe

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Xiaobing Shi, Van Andel Institute, United States

Version history

  1. Received: March 28, 2022
  2. Preprint posted: May 30, 2022 (view preprint)
  3. Accepted: February 2, 2023
  4. Accepted Manuscript published: February 3, 2023 (version 1)
  5. Version of Record published: February 21, 2023 (version 2)

Copyright

© 2023, Miyashita et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Ryota Miyashita
  2. Atsuya Nishiyama
  3. Weihua Qin
  4. Yoshie Chiba
  5. Satomi Kori
  6. Norie Kato
  7. Chieko Konishi
  8. Soichiro Kumamoto
  9. Hiroko Kozuka-Hata
  10. Masaaki Oyama
  11. Yoshitaka Kawasoe
  12. Toshiki Tsurimoto
  13. Tatsuro S Takahashi
  14. Heinrich Leonhardt
  15. Kyohei Arita
  16. Makoto Nakanishi
(2023)
The termination of UHRF1-dependent PAF15 ubiquitin signaling is regulated by USP7 and ATAD5
eLife 12:e79013.
https://doi.org/10.7554/eLife.79013

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https://doi.org/10.7554/eLife.79013

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