Poster abstracts
Poster number 166 submitted by Lauren Woodward
Exploring role of non-canonical exon junction complexes in human nonsense-mediated mRNA decay
Lauren Woodward (Department of Molecular Genetics, The Ohio State University), Justin Mabin (Department of Molecular Genetics, The Ohio State University), Robert Patton (Department of Physics, The Ohio State University), Ralf Bundschuh (Department of Physics, Division of Hematology, College of Medicine, Center for RNA Biology, The Ohio State University), Guramrit Singh (Department of Molecular Genetics, Center for RNA Biology, The Ohio State University)
Abstract:
The exon junction complex (EJC)—a multi-protein complex composed of eIF4AIII, Y14 and Magoh—is characterized by its deposition ~24nt upstream of exon-exon junctions. However, recent transcriptome-wide analyses of EJC binding in human cells by multiple laboratories has revealed that EJC is frequently detected at locations other than the canonical -24nt position. Such EJC occupancy at the so-called non-canonical (nc) sites is puzzling in light of the prevailing view of EJC occupancy based on in vitro studies, which supports a splicing-dependent and sequence-independent EJC deposition almost exclusively at -24 position. Aside from their differences in position, ncEJCs protect longer stretches of RNA than cEJCs, suggesting that ncEJCs may associate with additional proteins. ncEJCs are widespread, binding the first exon, internal exons, 3’UTRs and even some intronless mRNAs. Analysis of ncEJC footprints located in internal exons has revealed an enrichment of SR-protein binding motifs, suggesting some ncEJCs are represent binding of SR-proteins in tight interactions with EJC. However, some ncEJCs are bona fide eIF4AIII-binding sites as revealed by direct crosslinking of eIF4AIII to these sites via CLIP-seq. Like the numerous roles of cEJCs in post-transcriptional gene regulation, ncEJCs would also be expected to contribute to mRNA processing and turnover. EJCs are well known to trigger nonsense-mediated mRNA degradation (NMD) when present downstream of a stop codon. To begin to address the origin and function of ncEJCs, we are focusing on ncEJCs that occur in 3'UTR regions and hence could activate NMD. We identified many endogenous mRNAs from HEK293 cells that undergo NMD and bear ncEJCs in their 3’UTRs, but lack classical NMD-inducing features. We have validated that some of these NMD targets are indeed up-regulated upon eIF4AIII depletion. We are currently testing the hypothesis that a sub-set of ncEJCs are similar to cEJCs in their composition and biological function.
Keywords: EJC, noncanonical EJC, NMD