The Chd1 chromatin remodeler shifts hexasomes unidirectionally

  1. Robert F Levendosky
  2. Anton Sabantsev
  3. Sebastian Deindl
  4. Gregory D Bowman  Is a corresponding author
  1. Johns Hopkins University, United States
  2. Uppsala University, Sweden

Abstract

Despite their canonical two-fold symmetry, nucleosomes in biological contexts are often asymmetric: functionalized with post-translational modifications (PTMs), substituted with histone variants, and even lacking H2A/H2B dimers. Here we show that the Widom 601 nucleosome positioning sequence can produce hexasomes in a specific orientation on DNA, which provide a useful tool for interrogating chromatin enzymes and allow for the generation of precisely defined asymmetry in nucleosomes. Using this methodology, we demonstrate that the Chd1 chromatin remodeler from Saccharomyces cerevisiae requires H2A/H2B on the entry side for sliding, and thus, unlike the back-and-forth sliding observed for nucleosomes, Chd1 shifts hexasomes unidirectionally. Chd1 takes part in chromatin reorganization surrounding transcribing RNA polymerase II (Pol II), and using asymmetric nucleosomes we show that ubiquitin-conjugated H2B on the entry side stimulates nucleosome sliding by Chd1. We speculate that biased nucleosome and hexasome sliding due to asymmetry contributes to the packing of arrays observed in vivo.

Article and author information

Author details

  1. Robert F Levendosky

    T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Anton Sabantsev

    Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  3. Sebastian Deindl

    Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  4. Gregory D Bowman

    T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
    For correspondence
    gregory.dean.bowman@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8025-4315

Funding

National Institutes of Health (R01-GM084192)

  • Gregory D Bowman

Vetenskapsrådet

  • Sebastian Deindl

Knut och Alice Wallenbergs Stiftelse

  • Sebastian Deindl

National Institutes of Health (T32-GM007231)

  • Robert F Levendosky

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

Publication history

  1. Received: September 7, 2016
  2. Accepted: December 28, 2016
  3. Accepted Manuscript published: December 29, 2016 (version 1)
  4. Version of Record published: January 11, 2017 (version 2)

Copyright

© 2016, Levendosky 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. Robert F Levendosky
  2. Anton Sabantsev
  3. Sebastian Deindl
  4. Gregory D Bowman
(2016)
The Chd1 chromatin remodeler shifts hexasomes unidirectionally
eLife 5:e21356.
https://doi.org/10.7554/eLife.21356

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