Analysis of NRAS RNA G-quadruplex binding proteins reveals DDX3X as a novel interactor of cellular G-quadruplex containing transcripts. Issue 21 (26th September 2018)

• Record Type: Journal Article
• Authors: Herdy, Barbara; Mayer, Clemens; Varshney, Dhaval; Marsico, Giovanni; Murat, Pierre; Taylor, Chris; D'Santos, Clive; Tannahill, David; Balasubramanian, Shankar
• Is Part Of: Nucleic acids research. Volume 46:Issue 21(2018)
• Page Start: 11592
• Page End: 11604
• Publication Date: 2018-09-26
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gky861
• Languages: English
• ISSNs: 0305-1048

Abstract

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.