Transcriptome-wide identification of transient RNA G-quadruplexes in human cells.

TitleTranscriptome-wide identification of transient RNA G-quadruplexes in human cells.
Publication TypeJournal Article
Year of Publication2018
AuthorsYang SY, Lejault P, Chevrier S, Boidot R, A Robertson G, M Y Wong J, Monchaud D
JournalNat Commun
Volume9
Issue1
Pagination4730
Date Published11/2018
ISSN2041-1723
Abstract

Guanine-rich RNA sequences can fold into four-stranded structures, termed G-quadruplexes (G4-RNAs), whose biological roles are poorly understood, and in vivo existence is debated. To profile biologically relevant G4-RNA in the human transcriptome, we report here on G4RP-seq, which combines G4-RNA-specific precipitation (G4RP) with sequencing. This protocol comprises a chemical crosslinking step, followed by affinity capture with the G4-specific small-molecule ligand/probe BioTASQ, and target identification by sequencing, allowing for capturing global snapshots of transiently folded G4-RNAs. We detect widespread G4-RNA targets within the transcriptome, indicative of transient G4 formation in living human cells. Using G4RP-seq, we also demonstrate that G4-stabilizing ligands (BRACO-19 and RHPS4) can change the G4 transcriptomic landscape, most notably in long non-coding RNAs. G4RP-seq thus provides a method for studying the G4-RNA landscape, as well as ways of considering the mechanisms underlying G4-RNA formation, and the activity of G4-stabilizing ligands.

DOI10.1038/s41467-018-07224-8
Alternate JournalNat Commun
PubMed ID30413703
PubMed Central IDPMC6226477