Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

  1. Ramasubramanian Sundaramoorthy
  2. Amanda L Hughes
  3. Hassane El-Mkami
  4. David G Norman
  5. Helder Ferreira
  6. Tom Owen-Hughes  Is a corresponding author
  1. University of Dundee, United Kingdom
  2. University of St Andrews, United Kingdom

Abstract

ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here we present structures of the Saccharomyces cerevisiae Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented.

Data availability

The EM structures generated have been deposited in EMDB and PDB under the accession codes EMD-4318, PDB 6FTX, EMD-4336, PDB 6G0L.

The following data sets were generated

Article and author information

Author details

  1. Ramasubramanian Sundaramoorthy

    Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Amanda L Hughes

    Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. Hassane El-Mkami

    School of Physics and Astronomy, University of St Andrews, St Andrews, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. David G Norman

    Nucelic Acids Structure Research Group, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7658-7720
  5. Helder Ferreira

    School of Biology, University of St Andrews, St Andrews, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. Tom Owen-Hughes

    Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
    For correspondence
    t.a.owenhughes@dundee.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0618-8185

Funding

Wellcome (95062)

  • Ramasubramanian Sundaramoorthy
  • Amanda L Hughes
  • Hassane El-Mkami
  • David G Norman
  • Tom Owen-Hughes

European Molecular Biology Organization (ALTF 380-2015)

  • Amanda L Hughes

Wellcome (94090)

  • Ramasubramanian Sundaramoorthy
  • Amanda L Hughes
  • Hassane El-Mkami
  • David G Norman
  • Tom Owen-Hughes

Wellcome (99149)

  • Ramasubramanian Sundaramoorthy
  • Amanda L Hughes
  • Hassane El-Mkami
  • David G Norman
  • Tom Owen-Hughes

Wellcome (97945)

  • Ramasubramanian Sundaramoorthy
  • Amanda L Hughes
  • Hassane El-Mkami
  • David G Norman
  • Tom Owen-Hughes

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

Reviewing Editor

  1. Geeta J Narlikar, University of California, San Francisco, United States

Version history

  1. Received: February 6, 2018
  2. Accepted: July 24, 2018
  3. Accepted Manuscript published: August 6, 2018 (version 1)
  4. Version of Record published: August 31, 2018 (version 2)

Copyright

© 2018, Sundaramoorthy 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. Ramasubramanian Sundaramoorthy
  2. Amanda L Hughes
  3. Hassane El-Mkami
  4. David G Norman
  5. Helder Ferreira
  6. Tom Owen-Hughes
(2018)
Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome
eLife 7:e35720.
https://doi.org/10.7554/eLife.35720

Share this article

https://doi.org/10.7554/eLife.35720

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