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
  • 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.