The RNF168 paralog RNF169 defines a new class of ubiquitylated-histone reader involved in the response to DNA damage

  1. Julianne Kitevski-LeBlanc
  2. Amélie Fradet-Turcotte
  3. Predrag Kukic
  4. Marcus D Wilson
  5. Guillem Portella
  6. Tairan Yuwen
  7. Stephanie Panier
  8. Shili Duan
  9. Marella D Canny
  10. Hugo van Ingen
  11. Cheryl H Arrowsmith
  12. John L Rubinstein
  13. Michele Vendruscolo
  14. Daniel Durocher  Is a corresponding author
  15. Lewis E Kay  Is a corresponding author
  1. University of Toronto, Canada
  2. Mount Sinai Hospital, Canada
  3. University of Cambridge, United Kingdom
  4. The Francis Crick Research Institute, United Kingdom
  5. Leiden University, Netherlands

Abstract

Site-specific histone ubiquitylation plays a central role in orchestrating the response to DNA double-strand breaks (DSBs). DSBs elicit a cascade of events controlled by the ubiquitin ligase RNF168, which promotes the accumulation of repair factors such as 53BP1 and BRCA1 on the chromatin flanking the break site. RNF168 also promotes its own accumulation, and that of its paralog RNF169, but how they recognize ubiquitylated chromatin is unknown. Using methyl-TROSY solution NMR spectroscopy and molecular dynamics simulations, we present an atomic resolution model of human RNF169 binding to a ubiquitylated nucleosome, and validate it by electron cryomicroscopy. We establish that RNF169 binds to ubiquitylated H2A-Lys13/Lys15 in a manner that involves its canonical ubiquitin-binding helix and a pair of arginine-rich motifs that interact with the nucleosome acidic patch. This three-pronged interaction mechanism is distinct from that by which 53BP1 binds to ubiquitylated H2A-Lys15 highlighting the diversity in site-specific recognition of ubiquitylated nucleosomes.

Article and author information

Author details

  1. Julianne Kitevski-LeBlanc

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  2. Amélie Fradet-Turcotte

    The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  3. Predrag Kukic

    Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Marcus D Wilson

    The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9551-5514
  5. Guillem Portella

    Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. Tairan Yuwen

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3504-7995
  7. Stephanie Panier

    The Francis Crick Research Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  8. Shili Duan

    Structural Genomics Consortium, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  9. Marella D Canny

    Department of Medical Biophysics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  10. Hugo van Ingen

    Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  11. Cheryl H Arrowsmith

    Department of Medical Biophysics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  12. John L Rubinstein

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0566-2209
  13. Michele Vendruscolo

    Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3616-1610
  14. Daniel Durocher

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    For correspondence
    durocher@lunenfeld.ca
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3863-8635
  15. Lewis E Kay

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    For correspondence
    kay@pound.med.utoronto.ca
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4054-4083

Funding

Canadian Institutes of Health Research (RN203972 - 310401)

  • Lewis E Kay

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

Reviewing Editor

  1. Ivan Dikic, Goethe University School of Medicine, Germany

Publication history

  1. Received: December 2, 2016
  2. Accepted: April 12, 2017
  3. Accepted Manuscript published: April 13, 2017 (version 1)
  4. Version of Record published: May 11, 2017 (version 2)

Copyright

© 2017, Kitevski-LeBlanc 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. Julianne Kitevski-LeBlanc
  2. Amélie Fradet-Turcotte
  3. Predrag Kukic
  4. Marcus D Wilson
  5. Guillem Portella
  6. Tairan Yuwen
  7. Stephanie Panier
  8. Shili Duan
  9. Marella D Canny
  10. Hugo van Ingen
  11. Cheryl H Arrowsmith
  12. John L Rubinstein
  13. Michele Vendruscolo
  14. Daniel Durocher
  15. Lewis E Kay
(2017)
The RNF168 paralog RNF169 defines a new class of ubiquitylated-histone reader involved in the response to DNA damage
eLife 6:e23872.
https://doi.org/10.7554/eLife.23872

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