Best practices for the visualization, mapping, and manipulation of R-loops

Frédéric Chédin, Stella R. Hartono, Lionel A. Sanz, Vincent Vanoosthuyse

Research output: Contribution to journalReview articlepeer-review

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.

Original languageEnglish (US)
Article numbere106394
JournalEMBO Journal
Volume40
Issue number4
DOIs
StatePublished - Feb 15 2021

Keywords

  • DNA hybrid
  • DRIP
  • R-loops
  • RNA
  • RNase H1
  • S9.6 antibody

ASJC Scopus subject areas

  • Neuroscience(all)
  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

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