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

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. Mapping R-loop structures using bisDRIP-seq. Standard bisDRIP-seq was performed in thirteen control-treated samples. Two samples were generated from cells treated with the transcription inhibitor triptolide. The R-loop signal from bisDRIP-seq experiment was shown to be RNase H-sensitive using RNase H and matched-control bisDRIP-seq experiments. For each sample, reads on the "CTOB" strand are in the positive orientation and reads on the "CTOT" strand are in the negative orientation.