Poster abstracts
Poster number 91 submitted by Savannah Mills
Contribution of mRNA 3’ UTRs in substrate recognition by the nonsense-mediated mRNA decay pathway
Savannah F Mills (Department of Biochemistry, Case Western Reserve University), Kristian E Baker (Department of Genetics and Genome Sciences, Case Western Reserve University)
Abstract:
Nonsense-Mediated mRNA Decay (NMD) is a conserved RNA quality control process that identifies and rapidly degrades aberrant mRNAs harboring premature termination codons (PTCs), thereby preventing the expression of c-terminally truncated proteins. In addition to targeting PTC-containing mRNA, NMD also regulates the expression of hundreds of additional transcripts that encode full-length polypeptides. The mechanism by which the NMD machinery identifies its targets remains poorly understood; notwithstanding, key observations indicate that the length of RNA sequence downstream of a termination codon is an important determinant. Consistent with this, endogenous mRNAs lacking a nonsense codon but harboring lengthy 3’ untranslated regions (UTRs) are commonly regulated by the pathway. Despite this observation, a strict correlation between 3’ UTR length and NMD sensitivity at a transcriptome-wide level is lacking, indicating that additional RNA features contribute to discrimination between NMD sensitive and insensitive mRNAs.
As a means to generate a more comprehensive understanding of the mechanism underlying NMD substrate identification, we are characterizing long 3’ UTRs from endogenous yeast transcripts to identify RNA features that elicit, or confer resistance to, recognition by the NMD machinery. Preliminary data employing RNA immunoprecipitation of the core NMD factor, Upf1, confirms observations of a correlation between NMD sensitivity and the amount of Upf1 associated with mRNAs targeted to the NMD pathway. Notably, NMD insensitive mRNAs showed a drastic reduction in Upf1 association, despite harboring equivalently long 3’ UTRs. The observation that Upf1 fails to associate with these NMD insensitive mRNAs suggests that Upf1 is precluded from binding or stably associating with these transcripts. Ongoing studies are aimed at characterizing the mRNP compositions of these long 3’ UTRs and identifying cis-acting sequences and/or trans-acting factors involved in modulating Upf1 binding/association and transcript susceptibility to NMD.
Keywords: NMD, mRNA decay, 3 UTR