Abstract

RNA Polymerase II (Pol II) and transcription factors form concentrated hubs in cells via multivalent protein-protein interactions, often mediated by proteins with intrinsically disordered regions. During Herpes Simplex Virus infection, viral replication compartments (RCs) efficiently enrich host Pol II into membraneless domains, reminiscent of liquid-liquid phase-separation. Despite sharing several properties with phase-separated condensates, we show that RCs operate via a distinct mechanism wherein unrestricted nonspecific protein-DNA interactions efficiently outcompete host chromatin, profoundly influencing the way DNA binding proteins explore RCs. We find that the viral genome remains largely nucleosome-free, and this increase in accessibility allows Pol II and other DNA-binding proteins to repeatedly visit nearby DNA binding sites. This anisotropic behavior creates local accumulations of protein factors despite their unrestricted diffusion across RC boundaries. Our results reveal underappreciated consequences of nonspecific DNA binding in shaping gene activity, and suggest additional roles for chromatin in modulating nuclear function and organization.

Data availability

The GEO accession number for the ATAC-seq data is: GSE117335. The SPT trajectory data are available via Zenodo at DOI:10.5281/zenodo.1313872. The software used to generate these data is available at https://gitlab.com/tjian-darzacq-lab.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. David Trombley McSwiggen

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3844-7433
  2. Anders S Hansen

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  3. Sheila S Teves

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1220-2414
  4. Hervé Marie-Nelly

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  5. Yvonne Hao

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  6. Alec Basil Heckert

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  7. Kayla K Umemoto

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  8. Claire Dugast-Darzacq

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  9. Robert Tjian

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    For correspondence
    jmlim@berkeley.edu
    Competing interests
    Robert Tjian, is one of the three founding funders of eLife, and a member of eLife's Board of Directors.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0539-8217
  10. Xavier Darzacq

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    For correspondence
    darzacq@berkeley.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2537-8395

Funding

National Institutes of Health (UO1- 497 EB021236)

  • David Trombley McSwiggen
  • Anders S Hansen
  • Yvonne Hao
  • Alec Basil Heckert
  • Kayla K Umemoto
  • Claire Dugast-Darzacq
  • Xavier Darzacq

National Institutes of Health (U54-DK107980)

  • David Trombley McSwiggen
  • Anders S Hansen
  • Yvonne Hao
  • Alec Basil Heckert
  • Kayla K Umemoto
  • Claire Dugast-Darzacq
  • Xavier Darzacq

California Institute for Regenerative Medicine (LA1-08013)

  • Anders S Hansen
  • Alec Basil Heckert
  • Xavier Darzacq

Howard Hughes Medical Institute (003061)

  • David Trombley McSwiggen
  • Anders S Hansen
  • Sheila S Teves
  • Yvonne Hao
  • Alec Basil Heckert
  • Kayla K Umemoto
  • Robert Tjian

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

Reviewing Editor

  1. Jessica K Tyler, Weill Cornell Medicine, United States

Publication history

  1. Received: March 26, 2019
  2. Accepted: April 29, 2019
  3. Accepted Manuscript published: April 30, 2019 (version 1)
  4. Accepted Manuscript updated: May 7, 2019 (version 2)
  5. Version of Record published: May 16, 2019 (version 3)

Copyright

© 2019, McSwiggen 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. David Trombley McSwiggen
  2. Anders S Hansen
  3. Sheila S Teves
  4. Hervé Marie-Nelly
  5. Yvonne Hao
  6. Alec Basil Heckert
  7. Kayla K Umemoto
  8. Claire Dugast-Darzacq
  9. Robert Tjian
  10. Xavier Darzacq
(2019)
Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation
eLife 8:e47098.
https://doi.org/10.7554/eLife.47098

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