Best practices for the visualization, mapping, and manipulation of R‐loops. (7th January 2021)

• Record Type: Journal Article
• Authors: Chédin, Frédéric; Hartono, Stella R; Sanz, Lionel A; Vanoosthuyse, Vincent
• Is Part Of: EMBO journal. Volume 40:Number 4(2021)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2021-01-07
• Subjects: DNA hybrid -- DRIP -- R‐loops -- RNA -- RNase H1 -- S9.6 antibody; Molecular biology -- Periodicals; 572.805
• DOI: 10.15252/embj.2020106394
• Languages: English
• ISSNs: 0261-4189

Abstract

Abstract: R‐loops represent an abundant class of large non‐B DNA structures in genomes. Even though they form transiently and at modest frequencies, interfering with R‐loop formation or dissolution has significant impacts on genome stability. Addressing the mechanism(s) of R‐loop‐mediated genome destabilization requires a precise characterization of their distribution in genomes. A number of independent methods have been developed to visualize and map R‐loops, but their results are at times discordant, leading to confusion. Here, we review the main existing methodologies for R‐loop mapping and assess their limitations as well as the robustness of existing datasets. We offer a set of best practices to improve the reproducibility of maps, hoping that such guidelines could be useful for authors and referees alike. Finally, we propose a possible resolution for the apparent contradictions in R‐loop mapping outcomes between antibody‐based and RNase H1‐based mapping approaches. Abstract : With the increasing appreciation of R‐loops as frequent non‐B DNA structures with large impact on genome function and stability, this commentary proposes general guidelines for their reproducible study with antibody or RNase H1‐based approaches.