ArticleProceedings of the National Academy of Sciences of the United States of America2025
Protein-mediated stabilization and nicking of the nontemplate DNA strand dramatically affect R-loop formation in vitro.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- APOBEC3B regulates HPV replication by inducing R-loop formation and DNA damage.PLoS pathogens · 2026Article
- APE1 Activity is Controlled by Non-G-Quadruplex Conformations in Single- and Double-Stranded G-Quadruplex Constructs.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Article
- Protein-mediated stabilization and nicking of the nontemplate DNA strand dramatically affect R-loop formation in vitro.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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Authors and funding
6 authors.
Funding
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 nontemplate strand DNA nicks are powerful initiators of R-loop formation, increasing R-loop frequencies by up to two orders of magnitude. Atomic force microscopy revealed that the nontemplate 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 distinct class of R-loops. Overall, this work highlights the importance of the displaced single-strand on R-loop initiation and dynamics.
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Registered trials
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