Branchpoint translocation by fork remodelers as a general mechanism of R-loop removal
Charlotte Hodson, Sylvie van Twest, Małgorzata Dylewska, Julienne J. O’Rourke, Winnie Tan, Vincent J. Murphy, Mannu Walia, Lara Abbouche, Jadwiga Nieminuszczy, Elyse Dunn, Rohan Bythell‐Douglas, Jörg Heierhorst, Wojciech Niedźwiedź, Andrew J. Deans
Abstract
Co-transcriptional R loops arise from stalling of RNA polymerase, leading to the formation of stable DNA:RNA hybrids. Unresolved R loops promote genome instability but are counteracted by helicases and nucleases. Here, we show that branchpoint translocases are a third class of R-loop-displacing enzyme in vitro. In cells, deficiency in the Fanconi-anemia-associated branchpoint translocase FANCM causes R-loop accumulation, particularly after treatment with DNA:RNA-hybrid-stabilizing agents. This correlates with FANCM localization at R-loop-prone regions of the genome. Moreover, other branchpoint translocases associated with human disease, such as SMARCAL1 and ZRANB3, and those from lower organisms can also remove R loops in vitro. Branchpoint translocases are more potent than helicases in resolving R loops, indicating their evolutionary important role in R-loop suppression. In human cells, FANCM, SMARCAL1, and ZRANB3 depletion causes additive effects on R-loop accumulation and DNA damage. Our work reveals a mechanistic basis for R-loop displacement that is linked to genome stability.