Approaches for Mapping and Analysis of R-loops

Curr Protoc. 2024 Apr;4(4):e1037. doi: 10.1002/cpz1.1037.

Abstract

R-loops are nucleic acid structures composed of a DNA:RNA hybrid with a displaced non-template single-stranded DNA. Current approaches to identify and map R-loop formation across the genome employ either an antibody targeted against R-loops (S9.6) or a catalytically inactivated form of RNase H1 (dRNH1), a nuclease that can bind and resolve DNA:RNA hybrids via RNA exonuclease activity. This overview article outlines several ways to map R-loops using either methodology, explaining the differences and similarities among the approaches. Bioinformatic analysis of R-loops involves several layers of quality control and processing before visualizing the data. This article provides resources and tools that can be used to accurately process R-loop mapping data and explains the advantages and disadvantages of the resources as compared to one another. © 2024 Wiley Periodicals LLC.

Keywords: RNase H1; R‐loops; S9.6; bioinformatics; sequencing.

Publication types

  • Review

MeSH terms

  • Computational Biology / methods
  • DNA / chemistry
  • Humans
  • R-Loop Structures*
  • RNA / chemistry
  • RNA / genetics
  • RNA / metabolism
  • Ribonuclease H* / chemistry
  • Ribonuclease H* / metabolism

Substances

  • Ribonuclease H
  • ribonuclease HI
  • DNA
  • RNA