Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation

Abstract
Data availability
Article and author information
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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

1. McSwiggen DT
2. Hansen AS
3. Teves S
4. Marie-Nelly H
5. Hao Y
6. Heckert AB
7. Umemoto KK
8. Dugast-Darzacq C
9. Tjian R
10. Darzacq X
(2018) Relative accessability of HSV1 genomic DNA compared with its host cell (ATAC-seq)
NCBI Gene Expression Omnibus, GSE117335.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117335
1. McSwiggen DT
2. Hansen AS
3. Teves S
4. Marie-Nelly H
5. Hao Y
6. Heckert AB
7. Umemoto KK
8. Dugast-Darzacq C
9. Tjian R
10. Darzacq X
(2018) Single Particle Tracking data for U2OS cells after infection
Zenodo, 10.5281/zenodo.1313872.

https://zenodo.org/record/1313872#.XKaU7y2ZPOQ

The following previously published data sets were used

1. Hansen AS
2. Woringer M
3. Grimm JB
4. Lavis LD
5. Tjian R
6. Darzacq X
(2017) Simulated data for 'Spot-On: robust model-based analysis of single-particle tracking experiments'
Zenodo, 10.5281/zenodo.835541.

https://zenodo.org/record/835541#.XKbKVS2ZPOR

Article and author information

Author details

David Trombley McSwiggen

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-3844-7433
Anders S Hansen

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States

Competing interests
No competing interests declared.
Sheila S Teves

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-1220-2414
Hervé Marie-Nelly

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States

Competing interests
No competing interests declared.
Yvonne Hao

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States

Competing interests
No competing interests declared.
Alec Basil Heckert

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States

Competing interests
No competing interests declared.
Kayla K Umemoto

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States

Competing interests
No competing interests declared.
Claire Dugast-Darzacq

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States

Competing interests
No competing interests declared.
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.

"This ORCID iD identifies the author of this article:" 0000-0003-0539-8217
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.

"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.

Copyright

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.