Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions

Synopsis image A single gene can give rise to many isoforms via alternative polyadenylation. This study demonstrates that isoforms of each gene can have different molecular phenotypes like RNA stability and interaction with proteins, diversifying the functional potential of the genome. Divergent post-transcriptional fates of 3 ' transcript isoforms are revealed at a genome-wide level. New techniques are presented that accurately measure isoform-specific stability and protein binding, thus demonstrating widespread variation in both. Even variations of a few nucleotides are associated with variations in transcript stability. Transcript binding to PUF3 and subsequent destabilization occurs in an isoform-specific manner. Abstract Recent research has uncovered extensive variability in the boundaries of transcript isoforms, yet the functional consequences of this variation remain largely unexplored. Here, we systematically discriminate between the molecular phenotypes of overlapping coding and non-coding transcriptional events from each genic locus using a novel genome-wide, nucleotide-resolution technique to quantify the half-lives of 3 ' transcript isoforms in yeast. Our results reveal widespread differences in stability among isoforms for hundreds of genes in a single condition, and that variation of even a single nucleotide in the 3 ' untranslated region (UTR) can affect transcript stability. While previous instances of negative associations between 3 ' UTR length and transcript stability have been reported, here, we find that shorter isoforms are not necessarily more stable. We demonstrate the role of RNA-protein interactions in conditioning isoform-specific stability, showing that PUF3 binds and destabilizes specific polyadenylation isoforms. Our findings indicate that although the functional elements of a gene are encoded in DNA sequence, the selective incorporation of these elements into RNA through transcript boundary variation allows a single gene to have diverse functional consequences.