1. Chromosomes and Gene Expression
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Asymmetry between the two acidic patches dictates the direction of nucleosome sliding by the ISWI chromatin remodeler

  1. Robert F Levendosky
  2. Gregory D Bowman  Is a corresponding author
  1. Johns Hopkins University, United States
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Cite this article as: eLife 2019;8:e45472 doi: 10.7554/eLife.45472

Abstract

The acidic patch is a functionally important epitope on each face of the nucleosome that affects chromatin remodeling. Although related by 2-fold symmetry of the nucleosome, each acidic patch is uniquely positioned relative to a bound remodeler. An open question is whether remodelers are distinctly responsive to each acidic patch. Previously we reported a method for homogeneously producing asymmetric nucleosomes with distinct H2A/H2B dimers (Levendosky et al., 2016). Here, we use this methodology to show that the Chd1 remodeler from Saccharomyces cerevisiae and ISWI remodelers from human and Drosophila have distinct spatial requirements for the acidic patch. Unlike Chd1, which is equally affected by entry- and exit-side mutations, ISWI remodelers strongly depend on the entry-side acidic patch. Remarkably, asymmetry in the two acidic patches stimulates ISWI to slide mononucleosomes off DNA ends, overriding the remodeler's preference to shift the histone core toward longer flanking DNA.

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.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5101-0810
  2. Gregory D Bowman

    T C Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
    For correspondence
    gdbowman@jhu.edu
    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 Institute of General Medical Sciences (R01-GM084192)

  • Robert F Levendosky
  • Gregory D Bowman

National Institutes of Health (R01-GM113240)

  • Robert F Levendosky
  • Gregory D Bowman

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: January 24, 2019
  2. Accepted: May 16, 2019
  3. Accepted Manuscript published: May 16, 2019 (version 1)
  4. Version of Record published: June 3, 2019 (version 2)

Copyright

© 2019, Levendosky & Bowman

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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Further reading

    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression
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    Tools and Resources Updated

    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, providing a useful tool for interrogating chromatin enzymes and allowing for the generation of nucleosomes with precisely defined asymmetry. 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.

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