Talk on Saturday 09:30-09:45am submitted by Laura de Lorenzo
The naturally-occurring non-stop mRNAs from Arabidopsis display relatively low stability
Laura de Lorenzo (Dept. of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA. ), Arthur G. Hunt (Dept. of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA. )
Non-stop decay is an mRNA surveillance pathway that ensure the rapid degradation of mRNA that lack a translational termination codon (1, 2). In plants, yeast, and mammals, polyadenylation sites have been shown to occur within protein-coding regions (3, 4). Such mRNAs would lack a translation termination codon and thus would constitute a class of naturally-occurring non-stop mRNAs. The significance of such mRNAs is not clear, and it is not known as they are, as a group, less functional than their full-length counterparts. Here, we used high-throughput sequencing to test the hypothesis that naturally-occurring non-stop mRNAs in Arabidopsis are less stable than the bulk of the mRNA population. Analysis of mRNAs with 3’ ends in different regions revealed that mRNAs that are polyadenylated within coding regions (non-stop mRNAs) and also within introns had lower relative stabilities than other mRNA isoforms. Interestingly, non-stop mRNAs were enriched in GA-repeat sequence motifs surrounding the poly(A) sites, and the set of genes that encode with non-stop mRNAs was enriched for those associated with regulatory functions. The GA-repeat motifs were found to be conserved in two Brassicaceae species and over-represented in non-stop mRNAs from Medicago truncatula. Our results suggest non-stop mRNAs constitute a mode of negative regulation in Arabidopsis, and that this mode of regulation is conserved in other plant species.
1. Frischmeyer PA, van Hoof A, O'Donnell K, Guerrerio AL, Parker R and Dietz HC. 2002. An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Science 295: 2258-2261.
2. van Hoof A, Frischmeyer PA, Dietz HC and Parker R. 2002. Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science, 295: 2262–2264.
3. Yoon OK and Brem RB. 2010. Noncanonical transcript forms in yeast and their regulation during environmental stress. RNA, 16: 1256-1267.
4. Wu W, Liu M, Downie B, Liang C, Ji G, Li QQ and Hunt AG. 2011. Genome-wide landscape of polyadenylation in Arabidopsis provides evidences for extensive alternative polyadenylation. PNAS, 108: 12533-12538.
Keywords: PAT-seq, non-stop mRNA, Alternative polyadenylation