Protein-mediated stabilization and nicking of the non-template DNA strand dramatically affect R-loop formation in vitro

Abstract

R-loops are an important class of non-B DNA structures that form co-transcriptionally. Using in vitro transcription and unbiased quantitative sequencing readouts, we show that the addition of single-strand DNA binding proteins co-transcriptionally can drive a 3- to 5-fold increase of R-loop frequency without significant changes to R-loop distribution. We propose that this is caused by stabilizing and preventing the collapse of short nascent R-loops. This suggests that R-loop formation is highly dynamic and highlights single strand binding proteins as players in cellular R-loop regulation. We further show that non-template strand DNA nicks are powerful initiators of R-loop formation, increasing R-loop frequencies by up to two orders of magnitude. Atomic force microscopy (AFM) revealed that the non-template strand in nick-initiated structures is often flayed away from the RNA:DNA hybrid and engaged in self-pairing, creating unique forked R-loop features. DNA nicks, one of the most frequent DNA lesions in cells, are therefore potential hotspots for opportunistic R-loop initiation and may cause the formation of a novel class of R-loops. Overall, this work highlights the importance of the displaced single-strand on R-loop initiation and dynamics. SIGNIFICANCE STATEMENTR-loops are three-stranded DNA:RNA hybrid structures that form during transcription and play critical roles in both gene regulation and genome stability. This study reveals that single-stranded DNA-binding protein (SSB) increases R-loop frequency by stabilizing nascent R-loops, revealing a role for this protein in R-loop dynamics. Additionally, single strand DNA breaks, common cellular lesions, are identified as potent initiators of R-loops, increasing their rate of formation by up to 100-fold. Using atomic force microscopy, the study uncovers unique forked structures in nick-initiated R-loops, representing a novel class of secondary R-loop structures. These findings provide new insights into how cellular factors and DNA damage influence R-loop formation, with implications for understanding genome instability in health and disease.