Cellular Type Is a Major Determinant of R-Loop Genomic Distribution

R-loops that contain a DNA:RNA hybrid and unpaired single-stranded DNA are important determinants of normal cell physiology and of the pathogenesis of numerous diseases. Although several different approaches to R-loop mapping in the genome have been developed, these techniques can produce conflicting results. In order to assess their robustness, a recent study by Chedin et al. compared the R-loop genomic distribution assessed using different methods in normal and cancer cell lines. Importantly, that study assumed a high degree of similarity between R-loop genomic distributions across different cellular types. Here, we compared DRIP datasets produced using the same protocol in different cell lines to show that only 26% of R-loop peaks are shared between chronic myeloid leukemia-derived HAP1 cells and human pluripotent stem cells. Meanwhile, HAP1-derived double knockout cell lines are characterized by much higher fractions of R-loop peaks that are identical both to each other (most of them) and to the R-loop peaks of their parental line (71 and 55%). We conclude that cellular type represents a major determinant of R-loop genomic distribution and, therefore, that only a systematic comparison of a large array of various cell/tissue type-derived R-loop datasets may address the inconsistencies between different R-loop mapping techniques.