Alternative polyadenylation diversifies post‐transcriptional regulation by selective RNA–protein interactions

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 0 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 0 untranslated region (UTR) can affect transcript stability. While previous instances of negative associations between 3 0 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.

The differential expression of alternatively polyadenylated transcripts is a common stress-induced response mechanism that modulates mammalian mRNA expression in a quantitative and qualitative fashion

“…′ UTR length to influence expression to a minor extent (Spies et al 2013;Gruber et al 2014;Gupta et al 2014). Differences in 3 ′ UTR length provoked by 3 ′ UTR-APA can, however, influence important functions of the mRNA without necessarily changing mRNA abundance, as has recently been highlighted by the finding that cellular proteins can bind to the 3 ′ UTR and thereby determine protein localization (Berkovits and Mayr 2015).…”

“…Early work on alternative polyadenylation in proliferating and cancer cells suggested that APA-provoked changes in 3 ′ UTR length inversely correlated with the expression levels of the respective mRNAs and proteins, likely caused by modified miRNA and RBP binding (Sandberg et al 2008;Mayr and Bartel 2009). This hypothesis was challenged by other studies that reported 3 ′ UTR length to have a limited effect on mRNA and protein expression levels in yeast and mice (Spies et al 2013;Gruber et al 2014;Gupta et al 2014). As a most interesting new dimension, a recent report implicated 3 ′ UTR-APA to influence the localization of newly translated proteins and thus described an essential cellular role of APA beyond modulating mRNA abundance (Berkovits and Mayr 2015).…”

Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast

“…4A, Materials and Methods). These include three described motifs: the Puf3 binding motif TGTAAATA (FDR = 3.2 × 10 −5 , median fold-change 1.29) (Gerber et al 2004;Gupta et al 2014), the Whi3 binding motif TGCAT (FDR = 7 × 10 −4 , median fold-change 1.24) (Colomina et al 2008;Cai and Futcher 2013), and a poly(U) motif TTTTTTA (FDR = 0.09, median fold-change 1.20), which can be bound by Pub1 (Duttagupta et al 2005), or is part of the long poly(U) stretch that forms a looping structure with a poly(A) tail (Geisberg et al 2014). Moreover, an uncharacterized motif, ATATTC, was associated with lower mRNA half-life (FDR = 2 × 10 −5 , median fold-change 1.24).…”

Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation

“…These include the U1 snRNP (Berg et al 2012), poly(A) binding protein (de Klerk et al 2012;Jenal et al 2012), the cytoplasmic cleavage and polyadenylation (CPEB1) factor (Bava et al 2013), cleavage factor I (Martin et al 2012;Masamha et al 2014), FIP1L1 (Lackford et al 2014), RBBP6 (Di Giammartino et al 2014), the elongation rate of RNA polymerase II (RNAPII) (Martincic et al 2009;Ji et al 2011;Pinto et al 2011), and several RNA-binding proteins (Al-Ahmadi et al 2009;Mansfield and Keene 2012;Liu et al 2013;Oktaba et al 2015). Although these studies have demonstrated the prevalence of APA in eukaryotic cells, the extent to which APA alters RNA metabolism has recently come into question (Spies et al 2013;Gupta et al 2014;Neve and Furger 2014).…”