2. Academic Validation
  3. Analysis of NRAS RNA G-quadruplex binding proteins reveals DDX3X as a novel interactor of cellular G-quadruplex containing transcripts

Analysis of NRAS RNA G-quadruplex binding proteins reveals DDX3X as a novel interactor of cellular G-quadruplex containing transcripts

  • Nucleic Acids Res. 2018 Nov 30;46(21):11592-11604. doi: 10.1093/nar/gky861.
Barbara Herdy 1,  Clemens Mayer 2 3,  Dhaval Varshney 1,  Giovanni Marsico 1,  Pierre Murat 1 3,  Chris Taylor 1 4,  Clive D'Santos 1,  David Tannahill 1,  Shankar Balasubramanian 1 3
Affiliations

Affiliations

  • 1 Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
  • 2 Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands.
  • 3 Department of Chemistry, University of Cambridge Lensfield Road, Cambridge CB2 1EW, UK.
  • 4 Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, UK.
PMID: 30256975 DOI: 10.1093/nar/gky861
Abstract

RNA G-quadruplexes (rG4s) are secondary structures in mRNAs known to influence RNA post-transcriptional mechanisms thereby impacting neurodegenerative disease and Cancer. A detailed knowledge of rG4-protein interactions is vital to understand rG4 function. Herein, we describe a systematic affinity proteomics approach that identified 80 high-confidence interactors that assemble on the rG4 located in the 5'-untranslated region (UTR) of the NRAS oncogene. Novel rG4 interactors included DDX3X, DDX5, DDX17, GRSF1 and NSUN5. The majority of identified proteins contained a glycine-arginine (GAR) domain and notably GAR-domain mutation in DDX3X and DDX17 abrogated rG4 binding. Identification of DDX3X targets by transcriptome-wide individual-nucleotide resolution UV-crosslinking and affinity enrichment (iCLAE) revealed a striking association with 5'-UTR rG4-containing transcripts which was reduced upon GAR-domain mutation. Our work highlights hitherto unrecognized features of rG4 structure-protein interactions that highlight new roles of rG4 structures in mRNA post-transcriptional control.

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