Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq

Abstract
Data availability
Article and author information
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Abstract

R-loops are features of chromatin consisting of a strand of DNA hybridized to RNA, as well as the expelled complementary DNA strand. R-loops are enriched at promoters where they have recently been shown to have important roles in modifying gene expression. However, the location of promoter-associated R-loops and the genomic domains they perturb to modify gene expression remain unclear. To resolve this issue, we developed a bisulfite-based approach, bisDRIP-seq, to map R-loops across the genome at near-nucleotide resolution in MCF-7 cells. We found the location of promoter-associated R-loops is dependent on the presence of introns. In intron-containing genes, R-loops are bounded between the transcription start site and the first exon-intron junction. In intronless genes, the 3' boundary displays gene-specific heterogeneity. Moreover, intronless genes are often associated with promoter-associated R-loop formation. Together, these studies provide a high-resolution map of R-loops and identify gene structure as a critical determinant of R-loop formation.

Data availability

The following data sets were generated

1. Dumelie JG
2. Jaffrey SR
(2017) Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq
GSE98886.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98886

The following previously published data sets were used

1. Sanz LA
2. Lim Y
3. Hartono SR
4. Rajpurkar AR
5. Chedin F
(2016) Human and mouse DRIP-seq and DRIPc-seq
GSE70189.

https://www.ncbi.nlm.nih.gov/pubmed/22955987
1. ENCODE (Carninci Lab)
(2012) CAGE on human MCF-7 nucleus long polyadenylated RNA
ENCFF207DXM.

https://www.encodeproject.org/experiments/ENCSR000CKV/
1. ENCODE (Graveley Lab)
(2016) RNA Evaluation MCF7 Long Total from Graveley
ENCFF426WXY.

https://www.encodeproject.org/experiments/ENCSR667JTA/
1. ENCODE (Graveley Lab)
(2016) RNA Evaluation MCF7 Long Total from Graveley
ENCFF866OVQ.

https://www.encodeproject.org/experiments/ENCSR667JTA/
1. Hah N
2. Murakami S
3. Nagari A
4. Danko CG
5. Kraus WL
(2013) Enhancer Transcripts Mark Active Estrogen Receptor Binding Sites
GSE43835.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43835
1. ENCODE (Yeo Lab)
(2015) eCLIP experiment on HepG2 against SRSF1
ENCFF327NVE.

https://www.encodeproject.org/experiments/ENCSR989VIY/
1. ENCODE (Yeo Lab)
(2015) eCLIP experiment on K562 against SRSF1
ENCFF137IAG.

https://www.encodeproject.org/experiments/ENCSR432XUP/
1. ENCODE (Iyer Lab)
(2011) POLR2A ChIP-seq on human MCF-7
ENCSR000DMT.

https://www.encodeproject.org/experiments/ENCSR000DMT/
1. ENCODE (Gingeras Lab)
(2012) RNA-seq (polyA mRNA RNA-seq) on Homo sapiens MCF-7 nuclear fraction
ENCSR000CTO.

https://www.encodeproject.org/experiments/ENCSR000CTO/

Article and author information

Author details

Jason G Dumelie

Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, United States

Competing interests
The authors declare that no competing interests exist.
Samie R Jaffrey

Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, United States

For correspondence
srj2003@med.cornell.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-3615-6958

Funding

Starr Foundation (WC2015-011)

Jason G Dumelie

National Institutes of Health (R01 CA186702)

Samie R Jaffrey

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.