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Review
. 2022 Mar;17(3):870-889.
doi: 10.1038/s41596-021-00671-6. Epub 2022 Feb 9.

Global mapping of RNA G-quadruplexes (G4-RNAs) using G4RP-seq

Sunny Y Yang  1 , David Monchaud  2 , Judy M Y Wong  3
Affiliations
Review

Global mapping of RNA G-quadruplexes (G4-RNAs) using G4RP-seq

Sunny Y Yang et al. Nat Protoc. 2022 Mar.

Abstract

Guanine-rich RNAs can fold into four-stranded structures, termed G-quadruplexes (G4-RNAs), and participate in a wide range of biological processes. Here we describe in detail a G4-RNA-specific precipitation (G4RP) protocol, which enables the transcriptomic profiling of G4-RNAs. The G4RP protocol consists of a chemical cross-linking step, followed by affinity capture with a G4-specific probe, BioTASQ. G4RP can be coupled with sequencing to capture a comprehensive global snapshot of folded G4-RNAs. This method can also be used to profile induced changes (i.e., through G4 ligand treatments) within the G4-RNA transcriptome. The entire protocol can be completed in 1-2 weeks and can be scaled up or down depending on the specific experimental goals. In addition to the protocol details, we also provide here a guide for optimization in different laboratory setups.

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