1. Biochemistry and Chemical Biology
  2. Structural Biology and Molecular Biophysics
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DNA-mediated association of two histone-bound CAF-1 complexes drives tetrasome assembly in the wake of DNA replication

  1. Francesca Mattiroli
  2. Yajie Gu
  3. Tejas Yadav
  4. Jeremy L Balsbaugh
  5. Michael R Harris
  6. Eileen S Findlay
  7. Yang Liu
  8. Catherine A Radebaugh
  9. Laurie A Stargell
  10. Natalie G Ahn
  11. Iestyn Whitehouse
  12. Karolin Luger  Is a corresponding author
  1. Howard Hughes Medical Institute, University of Colorado, Boulder, United States
  2. Weill Cornell Graduate School of Medical Sciences, United States
  3. University of Colorado, Boulder, United States
  4. Memorial Sloan Kettering Cancer Center, United States
  5. Colorado State University, United States
Research Article
  • Cited 33
  • Views 2,961
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Cite this article as: eLife 2017;6:e22799 doi: 10.7554/eLife.22799

Abstract

Nucleosome assembly in the wake of DNA replication is a key process that regulates cell identity and survival. Chromatin assembly factor 1 (CAF-1) is a H3-H4 histone chaperone that associates with the replisome and orchestrates chromatin assembly following DNA synthesis. Little is known about the mechanism and structure of this key complex. Here we investigate the CAF-1•H3-H4 binding mode and the mechanism of nucleosome assembly. We show that CAF-1 binding to a H3-H4 dimer activates the Cac1 winged helix domain interaction with DNA. This drives the formation of a transient CAF-1•histone•DNA intermediate containing two CAF-1 complexes, each associated with one H3-H4 dimer. Here, the (H3-H4)2 tetramer is formed and deposited onto DNA. Our work elucidates the molecular mechanism for histone deposition by CAF-1, a reaction that has remained elusive for other histone chaperones, and it advances our understanding of how nucleosomes and their epigenetic information are maintained through DNA replication.

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Author details

  1. Francesca Mattiroli

    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1574-7217

  2. Yajie Gu

    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Tejas Yadav

    Weill Cornell Graduate School of Medical Sciences, New York, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Jeremy L Balsbaugh

    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Michael R Harris

    Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Eileen S Findlay

    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Yang Liu

    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Catherine A Radebaugh

    Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
    Competing interests
    The authors declare that no competing interests exist.

  9. Laurie A Stargell

    Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
    Competing interests
    The authors declare that no competing interests exist.

  10. Natalie G Ahn

    Biofrontiers Institute, University of Colorado, Boulder, Boulder, United States
    Competing interests
    The authors declare that no competing interests exist.

  11. Iestyn Whitehouse

    Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0385-3116

  12. Karolin Luger

    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, United States
    For correspondence
    karolin.luger@colorado.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5136-5331

Funding

Howard Hughes Medical Institute (Investigator)

  • Karolin Luger

National Institute of General Medical Sciences (GM067777)

  • Karolin Luger

European Molecular Biology Organization (ALTF 1267-2013)

  • Francesca Mattiroli

KWF Kankerbestrijding (2014-6649)

  • Francesca Mattiroli

National Science Foundation (MCB-1330019)

  • Laurie A Stargell

National Institute of General Medical Sciences (GM114594)

  • Natalie G Ahn

National Institute of General Medical Sciences (GM102253)

  • Iestyn Whitehouse

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

Reviewing Editor

  1. Paul D. Kaufman, U. Massachusetts Medical School, United States

Publication history

  1. Received: October 29, 2016
  2. Accepted: March 14, 2017
  3. Accepted Manuscript published: March 18, 2017 (version 1)
  4. Version of Record published: April 25, 2017 (version 2)
  5. Version of Record updated: February 12, 2018 (version 3)

Copyright

© 2017, Mattiroli 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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    How the very first step in nucleosome assembly, deposition of histone H3-H4 as tetramers or dimers on DNA, is accomplished remains largely unclear. Here, we report that yeast chromatin assembly factor 1 (CAF1), a conserved histone chaperone complex that deposits H3-H4 during DNA replication, binds a single H3-H4 heterodimer in solution. We identify a new DNA-binding domain in the large Cac1 subunit of CAF1, which is required for high-affinity DNA binding by the CAF1 three-subunit complex, and which is distinct from the previously described C-terminal winged-helix domain. CAF1 binds preferentially to DNA molecules longer than 40 bp, and two CAF1-H3-H4 complexes concertedly associate with DNA molecules of this size, resulting in deposition of H3-H4 tetramers. While DNA binding is not essential for H3–H4 tetrasome deposition in vitro, it is required for efficient DNA synthesis-coupled nucleosome assembly. Mutant histones with impaired H3-H4 tetramerization interactions fail to release from CAF1, indicating that DNA deposition of H3-H4 tetramers by CAF1 requires a hierarchical cooperation between DNA binding, H3-H4 deposition and histone tetramerization.

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