Journal
NATURE COMMUNICATIONS
Volume 9, Issue -, Pages -Publisher
NATURE RESEARCH
DOI: 10.1038/s41467-018-07224-8
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Funding
- Agence Nationale de la Recherche [ANR-17-CE17-0010-01]
- European Research Council, is part of the project Pharmacoimagerie AMP
- agents theranostiques - Universite de Bourgogne Franche-Comte [H2020-MSCA-IF-2016-750368]
- European Research Council, is part of the project Pharmacoimagerie AMP
- agents theranostiques - Conseil Regional de Bourgogne (PARI) [H2020-MSCA-IF-2016-750368]
- European Union
- University of British Columbia
- Agence Nationale de la Recherche (ANR) [ANR-17-CE17-0010] Funding Source: Agence Nationale de la Recherche (ANR)
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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.
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