Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome

  1. Luka Bacic
  2. Guillaume Gaullier
  3. Anton Sabantsev
  4. Laura C Lehmann
  5. Klaus Brackmann
  6. Despoina Dimakou
  7. Mario Halic
  8. Graeme Hewitt
  9. Simon Boulton
  10. Sebastian Deindl  Is a corresponding author
  1. Uppsala University, Sweden
  2. St Jude Children's Research Hospital, United States
  3. The Francis Crick Institute, United Kingdom

Abstract

The chromatin remodeler ALC1 is recruited to and activated by DNA damage-induced poly(ADP-ribose) (PAR) chains deposited by PARP1/PARP2/HPF1 upon detection of DNA lesions. ALC1 has emerged as a candidate drug target for cancer therapy as its loss confers synthetic lethality in homologous recombination-deficient cells. However, structure-based drug design and molecular analysis of ALC1 have been hindered by the requirement for PARylation and the highly heterogeneous nature of this post-translational modification. Here, we reconstituted an ALC1 and PARylated nucleosome complex modified in vitro using PARP2 and HPF1. This complex was amenable to cryo-EM structure determination without cross-linking, which enabled visualization of several intermediate states of ALC1 from the recognition of the PARylated nucleosome to the tight binding and activation of the remodeler. Functional biochemical assays with PARylated nucleosomes highlight the importance of nucleosomal epitopes for productive remodeling and reveal that ALC1 preferentially slides nucleosomes away from DNA breaks.

Data availability

The cryo-EM map of the ALC1-nucleosome complex in the active state was deposited at the EMDB with accession code EMD-13065. The model of the ALC1-nucleosome complex in the active state was deposited at the PDB with accession code 7OTQ. The map series from the cryoDRGN graph traversal was deposited at the EMDB with accession code EMD-13070. Raw movies, extracted particles and their coordinates, and cryoDRGN and cryoSPARC job directories were deposited in EMPIAR with accession code EMPIAR-10739.

Article and author information

Author details

  1. Luka Bacic

    Uppsala University, Uppsala, Sweden
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6896-3506
  2. Guillaume Gaullier

    Uppsala University, Uppsala, Sweden
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3405-6021
  3. Anton Sabantsev

    Uppsala University, Uppsala, Sweden
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8559-8894
  4. Laura C Lehmann

    Uppsala University, Uppsala, Sweden
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2518-5606
  5. Klaus Brackmann

    Uppsala University, Uppsala, Sweden
    Competing interests
    No competing interests declared.
  6. Despoina Dimakou

    Uppsala University, Uppsala, Sweden
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1424-5469
  7. Mario Halic

    St Jude Children's Research Hospital, Memphis, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0061-7372
  8. Graeme Hewitt

    The Francis Crick Institute, London, United Kingdom
    Competing interests
    No competing interests declared.
  9. Simon Boulton

    The Francis Crick Institute, London, United Kingdom
    Competing interests
    Simon Boulton, is co-founder and VP Science Strategy at Artios Pharma Ltd..
  10. Sebastian Deindl

    Uppsala University, Uppsala, Sweden
    For correspondence
    sebastian.deindl@icm.uu.se
    Competing interests
    Sebastian Deindl, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6807-8654

Funding

European Research Council (714068)

  • Sebastian Deindl

Knut och Alice Wallenbergs Stiftelse (KAW 019.0306)

  • Sebastian Deindl

Vetenskapsrådet (VR Grant 2019-03534)

  • Sebastian Deindl

Cancerfonden (19 0055 Pj)

  • Sebastian Deindl

Cancer Research UK (FC0010048)

  • Simon Boulton

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

Reviewing Editor

  1. Jerry L Workman, Stowers Institute for Medical Research, United States

Version history

  1. Preprint posted: June 18, 2021 (view preprint)
  2. Received: June 18, 2021
  3. Accepted: September 5, 2021
  4. Accepted Manuscript published: September 6, 2021 (version 1)
  5. Version of Record published: September 24, 2021 (version 2)

Copyright

© 2021, Bacic 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. Luka Bacic
  2. Guillaume Gaullier
  3. Anton Sabantsev
  4. Laura C Lehmann
  5. Klaus Brackmann
  6. Despoina Dimakou
  7. Mario Halic
  8. Graeme Hewitt
  9. Simon Boulton
  10. Sebastian Deindl
(2021)
Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome
eLife 10:e71420.
https://doi.org/10.7554/eLife.71420

Share this article

https://doi.org/10.7554/eLife.71420

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