3′ UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts

Abstract

Variation in protein output across the genome is controlled at several levels, but the relative contributions of different regulatory mechanisms remain poorly understood. Here, we obtained global measurements of decay and translation rates for mRNAs with alternative 39 untranslated regions (39 UTRs) in murine 3T3 cells. Distal tandem isoforms had slightly but significantly lower mRNA stability and greater translational efficiency than proximal isoforms on average. The diversity of alternative 39 UTRs also enabled inference and evaluation of both positively and negatively acting cisregulatory elements. The 39 UTR elements with the greatest implied influence were microRNA complementary sites, which were associated with repression of 32% and 4% at the stability and translational levels, respectively. Nonetheless, both the decay and translation rates were highly correlated for proximal and distal 39 UTR isoforms from the same genes, implying that in 3T3 cells, alternative 39 UTR sequences play a surprisingly small regulatory role compared to other mRNA regions.

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).…”

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).…”

Global 3′ UTR shortening has a limited effect on protein abundance in proliferating T cells

“…Initial studies suggested that the lack of microRNA (miRNA)-binding sites in the shortened 3 0 UTRs leads to an increased stability of the mRNAs and an increased protein output 3,4 . This conjecture was later refuted by a transcriptome-wide analysis that was carried out in mouse embryonic fibroblasts, where small differences in the relative stability of 3 0 UTR isoforms were found 8 . MiRNAs are only one class of regulators that act on 3 0 UTRs, guiding the RNA-induced silencing complexes to target mRNAs to increase their decay rate and reduce translation 9,10 .…”