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Nat Commun. 2018 Nov 9;9(1):4730. doi: 10.1038/s41467-018-07224-8.

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

Author information

1
Faculty of Pharmaceutical Sciences, University of British Columbia, Pharmaceutical Sciences Building, 2405 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada.
2
Institut de Chimie Moléculaire (ICMUB), UBFC Dijon, CNRS UMR6302, 9, Rue Alain Savary, 21078, Dijon, France.
3
Platform of Transfer in Cancer Biology, Centre Georges-François Leclerc, BP 77980, 1, Rue Professeur Marion, 21079, Dijon, France.
4
Genome Sciences Center, BC Cancer Agency, 570 W 7th Ave, Vancouver, BC, V5Z 4S6, Canada.
5
Faculty of Pharmaceutical Sciences, University of British Columbia, Pharmaceutical Sciences Building, 2405 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada. judy.wong@ubc.ca.
6
Institut de Chimie Moléculaire (ICMUB), UBFC Dijon, CNRS UMR6302, 9, Rue Alain Savary, 21078, Dijon, France. david.monchaud@cnrs.fr.

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.

PMID:
30413703
PMCID:
PMC6226477
DOI:
10.1038/s41467-018-07224-8
[Indexed for MEDLINE]
Free PMC Article

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