RHON1 Co-transcriptionally Resolves R-Loops for Arabidopsis Chloroplast Genome Maintenance

Abstract

Summary: Preventing transcription-replication head-on conflict (HO-TRC)-triggered R-loop formation is essential for maintaining genome integrity in bacteria, plants, and mammals. The R-loop eraser RNase H can efficiently relax HO-TRCs. However, it is not clear how organisms resist HO-TRC-triggered R-loops when RNase H proteins are deficient. By screening factors that may relieve R-loop accumulation in the Arabidopsis atrnh1c mutant, we find that overexpression of the R-loop helicase RHON1 can rescue the defects of aberrantly accumulated HO-TRC-triggered R-loops co-transcriptionally. In addition, we find that RHON1 interacts with and orchestrates the transcriptional activity of plastid-encoded RNA polymerases to release the conflicts between transcription and replication. Our study illustrates that organisms employ multiple mechanisms to escape HO-TRC-triggered R-loop accumulation and thus maintain genome integrity. : Preventing transcription-replication head-on conflict (HO-TRC)-triggered R-loops is essential for genome maintenance in bacteria, plants, and mammals. Yang et al. unveil a bacterial Rho-like DNA:RNA helicase, RHON1, that functions in parallel with RNase H1 to restrict HO-TRC-promoted R-loops and stabilize the genome in Arabidopsis chloroplasts, the endosymbiotic organelle that is essential for photosynthesis. Keywords: R-loops, transcription-replication conflicts, head-on, RHON1, organelle-encoded RNA polymerase, RNase H1