Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq
- Weill Cornell Medical College, Cornell University, United States
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.
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Article and author information
Author details
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.
Reviewing Editor
- Danny Reinberg, Howard Hughes Medical Institute, New York University School of Medicine, United States
Version history
- Received: May 3, 2017
- Accepted: October 22, 2017
- Accepted Manuscript published: October 26, 2017 (version 1)
- Version of Record published: November 28, 2017 (version 2)
Copyright
© 2017, Dumelie & Jaffrey
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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Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq
eLife 6:e28306.
https://doi.org/10.7554/eLife.28306
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