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

Sunny Y. Yang, Pauline Lejault, Sandy Chevrier, Romain Boidot, A. Gordon Robertson, Judy M. Y. Wong () and David Monchaud ()
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Sunny Y. Yang: University of British Columbia
Pauline Lejault: UBFC Dijon, CNRS UMR6302
Sandy Chevrier: Centre Georges-François Leclerc
Romain Boidot: Centre Georges-François Leclerc
A. Gordon Robertson: BC Cancer Agency
Judy M. Y. Wong: University of British Columbia
David Monchaud: UBFC Dijon, CNRS UMR6302

Nature Communications, 2018, vol. 9, issue 1, 1-11

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-018-07224-8

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