Transcription-replication conflict resolution by nuclear RNA interference

Nuclear RNA interference (RNAi) is required for heterochromatin silencing, but Dicer also promotes genome stability by releasing RNA polymerase at sites of replication stress. R-loops are three-stranded DNA:RNA structures that accumulate at transcription-replication (T-R) collisions. We show that in RNase H-deficient cells, which accumulate pathological R-loops, Dcr1 processes R-loops at transcriptional start sites (TSSs) and end sites (TESs), releasing paused RNA polymerase and accounting for small RNAs (sRNAs) resembling DNA-damage-associated sense sRNAs (sdRNAs) found in cancer cells. Genetic evidence implicates nascent transcription-associated R-loops in genome instability in the absence of Dicer, with the helicase domain providing catalytic function reminiscent of related archaeal helicases involved in replication. The RNase H homolog Argonaute (Ago1) promotes genome instability by binding R-loops, and its removal relieves replication stress. Analysis of replication intermediates, DNA and RNA 3' ends, and fork processivity genome wide indicates Dicer resolves head-on T-R collisions, consistent with an ancient origin in DNA replication.