Mapping R-Loops Using Catalytically Inactive RNaseH1 (R-ChIP)

Xuan Zhang; Yajing Hao; Xiang-Dong Fu

doi:10.1007/978-1-0716-2477-7_24

Mapping R-Loops Using Catalytically Inactive RNaseH1 (R-ChIP)

Methods Mol Biol. 2022:2528:359-372. doi: 10.1007/978-1-0716-2477-7_24.

Authors

Xuan Zhang¹, Yajing Hao¹, Xiang-Dong Fu²

Affiliations

¹ Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
² Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, CA, USA. xdfu@health.ucsd.edu.

PMID: 35704204
DOI: 10.1007/978-1-0716-2477-7_24

Abstract

R-loops, three-stranded structures containing double-stranded DNA invaded by single-stranded RNA, have been linked to diverse biological processes. They play important roles in regulating gene regulation and DNA repair, contributing to a wide range of diseases. Understanding the formation and dynamic regulation of R-loops is thus a gateway to address many fundamental questions in regulatory biology, which requires the elucidation of the R-loop landscape at the genome scale. To aid in such efforts, this article provides an overview on R-loop mapping strategies along with a detailed protocol based on the use of catalytically inactive RNaseH1, an evolutionarily conserved protein responsible for R-loop recognition and resolution.

Keywords: DNA damage; Immunoprecipitation; R-ChIP; R-loop; RNaseH1; Transcription.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

DNA / genetics
DNA Repair
Genome
R-Loop Structures*
RNA* / genetics
Transcription, Genetic

Substances

RNA
DNA