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

Elife. 2017 Oct 26;6:e28306. doi: 10.7554/eLife.28306.

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.

Keywords: R-loops; RNA/DNA hybrids; chromosomes; evolutionary biology; genes; genomics; human; introns; promoters; splicing; transcription.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Chromatin*
  • Chromosome Mapping
  • Humans
  • MCF-7 Cells
  • Nucleic Acid Hybridization*
  • Promoter Regions, Genetic*
  • Sequence Analysis, DNA

Substances

  • Chromatin