Genome-wide mapping reveals increased R-loops in topoisomerase III-beta-deficient human cells

Aberrant R-loops can cause genomic DNA damage. We mapped R-loops across the genomes of human colon carcinoma HCT116 and fibrosarcoma HT1080 cells deficient for topoisomerase III-beta (TOP3B) by performing DNA-RNA immunoprecipitation followed by high-throughput sequencing (DRIP-seq). Knocking out TOP3B globally increases pre-existing R-loops. The enriched R-loops in TOP3B-KO cells are widely distributed in intergenic, protein-coding, and non-coding RNA genes. Comparison of genomic R-loops from TOP3B- and TOP1-depleted cells demonstrates partially overlapping and complementary functions of TOP3B and topoisomerase 1 (TOP1) in suppressing R-loops. Global transcription analyses show that the increased R-loops do not significantly change transcript levels in TOP3B-KO cells. However, increased R-loops in TOP3B-KO cells are associated with G4-quadruplexes and a DNA damage phenotype (γH2AX foci). Altogether, these results demonstrate that TOP3B is needed for the suppression of deleterious R-loops, which otherwise lead to genomic breaks.