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


Type
Article
Change log
Authors
Herdy, Barbara 
Mayer, Clemens 
Varshney, Dhaval 
Marsico, Giovanni 
Murat, Pierre 
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.

Description
Keywords
5' Untranslated Regions, Cytoplasm, DEAD-box RNA Helicases, G-Quadruplexes, Genes, ras, HeLa Cells, Humans, Protein Domains, RNA, Messenger, Reproducibility of Results
Journal Title
Nucleic Acids Res
Conference Name
Journal ISSN
0305-1048
1362-4962
Volume Title
46
Publisher
Oxford University Press (OUP)
Sponsorship
Cancer Research UK (CB4330)
European Research Council (339778)
European Commission Horizon 2020 (H2020) Marie Sk?odowska-Curie actions (702476)
ERC