Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage

Abstract
Data availability
Article and author information
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Abstract

The hormone estrogen (E2) binds the estrogen receptor to promote transcription of E2-responsive genes in the breast and other tissues. E2 also has links to genomic instability, and elevated E2 levels are tied to breast cancer. Here, we show that E2 stimulation causes a rapid, global increase in the formation of R-loops, co-transcriptional RNA-DNA products, which in some instances have been linked to DNA damage. We show that E2-dependent R-loop formation and breast cancer rearrangements are highly enriched at E2-responsive genomic loci and that E2 induces DNA replication-dependent double-strand breaks (DSBs). Strikingly, many DSBs that accumulate in response to E2 are R-loop dependent. Thus, R-loops resulting from the E2 transcriptional response are a significant source of DNA damage. This work reveals a novel mechanism by which E2 stimulation leads to genomic instability and highlights how transcriptional programs play an important role in shaping the genomic landscape of DNA damage susceptibility.

Data availability

The following data sets were generated

1. Stork CT
2. Bocek M
3. Swigut T
4. Cimprich K
(2016) Genome-wide DRIP-seq in E2 stimulated MCF7 cells
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE81851).

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81851

The following previously published data sets were used

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2. Danko CG
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5. Siepel A
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(2011) Global Analysis of the Immediate Transcriptional Effects of Estrogen Signaling Reveals a Rapid, Extensive, and Transient Response
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE27463).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27463
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(2014) Genome-wide modelling of transcription kinetics reveals patterns of RNA processing delays
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE62789).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62789
(2015) High-throughput sequencing of DNA G-quadruplex structures in the human genome
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE63874).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63874
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2. Davies H
3. Staaf J
4. Ramakrishna M
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6. Zou X
7. Martincorena I
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(2016) Landscape of somatic mutations in 560 breast cancer whole-genome sequences
Publicly available at the European Genome-phenome Archive (accession no. EGAS00001001178).

https://www.ebi.ac.uk/ega/studies/EGAS00001001178

Article and author information

Author details

Caroline Townsend Stork

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States

Competing interests
The authors declare that no competing interests exist.
Michael Bocek

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States

Competing interests
The authors declare that no competing interests exist.
Madzia P Crossley

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States

Competing interests
The authors declare that no competing interests exist.
Julie Sollier

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States

Competing interests
The authors declare that no competing interests exist.
Lionel A Sanz

Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States

Competing interests
The authors declare that no competing interests exist.
Frédéric Chédin

Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States

Competing interests
The authors declare that no competing interests exist.
Tomek Swigut

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States

Competing interests
The authors declare that no competing interests exist.
Karlene A Cimprich

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States

For correspondence
cimprich@stanford.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-1937-2969

Funding

Susan G. Komen (IIR 12222368)

Karlene A Cimprich

National Institutes of Health (R01 GM119334)

Karlene A Cimprich

National Institutes of Health (R01 GM100489)

Karlene A Cimprich

National Institutes of Health (R01 GM094299)

Frédéric Chédin

National Science Foundation (Graduate Research Fellowship)

Caroline Townsend Stork

National Institutes of Health (Training Grant T32GM007276)

Caroline Townsend Stork

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.