1. Chromosomes and Gene Expression
  2. Genetics and Genomics

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
https://doi.org/10.7554/eLife.28306
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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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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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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.

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

Share this article

https://doi.org/10.7554/eLife.28306

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