Rat1 promotes premature transcription termination at R-loops

Abstract

Certain DNA sequences can adopt a non-B form in the genome that interfere with DNA-templated processes, including transcription. Among the sequences that are intrinsically difficult to transcribe are those that tend to form R-loops, three-stranded nucleic acid str uct ures f ormed b y a DNA-RNA hybrid and the displaced ssDNA. Here we compared the transcription of an endogenous gene with and without an R-loop-forming sequence inserted. We show that, in agreement with previous in vivo and in vitro analyses, transcription elongation is delayed by R-loops in y east. Importantly, w e demonstrate that the Rat1 transcription terminator factor facilitates transcription throughout such str uct ures by inducing premature termination of arrested RNAPIIs. We propose that RNase H degrades the RNA moiety of the hybrid, pro viding an entry site for Rat1. T hus, w e ha v e unco v ered an unanticipated function of Rat1 as a transcription restoring f actor opening up the possibility that it ma y also promote transcription through other genomic DNA str uct ures intrinsically difficult to transcribe. If R-loop-mediated transcriptional stress is not relie v ed b y Rat1, it will cause genomic inst abilit y, probably through the increase of transcription-replication conflicts, a deleterious situation that could lead to cancer.