Cellular stress alters 3’UTR landscape through alternative polyadenylation and isoform-specific degradation. Mus musculus

Most eukaryotic genes express alternative polyadenylation (APA) isoforms with different lengths of 3’ untranslated region (3’UTR). Here we show arsenic stress elicits global shortening of 3’UTRs through two mechanisms. First, stress leads to immediate shortening of 3’UTR due to preferential usage of proximal cleavage and polyadenylation sites (PASs), as revealed by 3’ end sequencing of newly made RNAs that are metabolically labeled with 4-thiouridine. Second, long 3’UTR isoforms are more rapidly degraded during recovery from stress as compared to short 3’UTR isoforms, further shortening 3’UTR lengths in the cell. Using ribonucleoprotein immunoprecipitation coupled with 3’ end sequencing (3’READS+RIP), we show that the RNA-binding protein T cell-restricted intracellular antigen-1 (Tia1) preferentially interacts with long 3’UTR isoforms via U-rich elements in alternative 3’UTR sequences, and the interaction correlates with stress granule (SG) association during stress and with mRNA decay during recovery from stress, indicating SG-mediated RNA clearance mechanism post stress. Importantly, genes whose 3’UTRs are shortened by APA during stress can evade stress-induced 3’UTR size-based mRNA degradation, leading to higher transcript abundance post stress. Moreover, proliferating and differentiated cells display different extents of 3’UTR shortening after stress, indicating cell type-specific of impact of stress on the 3’UTR landscape. Together, our data indicate that 3’UTR length plays important roles in gene expression in stressed cells, and APA functions as an adaptive stress response mechanism to preserve mRNAs. Overall design: 4 RNA-seq libraries from NIH3T3 cells for gene expression analysis; 4 3'READS libraries for analysis of APA using total RNA from NIH3T3 cells treated with sodium arsenite for 1h; 6 3'READS libraries for analysis of APA time course using total RNA from NIH3T3 cells treated with sodium arsenite for 1h and recovered for different amount of time; 8 3'READS libraries for analysis of APA isoform stability using 4sU metabolic labeling in NIH3T3 cells; 8 3'READS libraries for analysis of stress response of proliferating and differented C2C12 cells using cytoplasmic RNA; 4 3'READS libraries for the analysis of APA during C2C12 cell differentiation.