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

  1. Jason G Dumelie
  2. Samie R Jaffrey  Is a corresponding author
  1. 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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The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. 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.
  2. 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.
    ORCID icon "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.

Reviewing Editor

  1. Danny Reinberg, Howard Hughes Medical Institute, New York University School of Medicine, United States

Publication history

  1. Received: May 3, 2017
  2. Accepted: October 22, 2017
  3. Accepted Manuscript published: October 26, 2017 (version 1)
  4. 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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  1. Jason G Dumelie
  2. Samie R Jaffrey
(2017)
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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