Post-transcriptional gene regulation via crosstalk between alternative polyadenylation and endogenous double-stranded RNAs

Abstract

Alu elements are conserved repeat sequences of SINE retrotransposons and found abundantly in the non-coding regions of the primate genome. When pairs of inverted Alu repeats (IRAlus) are present in the 3' UTR, they form an intramolecular duplex structure that leads to the nuclear sequestration and subsequent translational suppression of the host mRNA. Despite the additive post-transcriptional regulatory layer, the physiological function of gene silencing by IRAlus remains unknown. Here, we combine alternative polyadenylation (APA) and J2 dsRNA-sequencing to investigate the gene regulation by IRAlus and other endogenous duplex structures. We find that incorporating APA information allows accurate identification of genes with functional IRAlus in the constitutive 3' UTR, which results in strong nuclear localization and translation suppression. By utilizing J2 dsRNA-sequencing, we greatly expand the number of genes that contain duplex elements that can induce gene silencing effects. Moreover, our approach reveals that genes involved in the protein ubiquitination pathway, in particular E3 ubiquitin ligase mouse double minute 2 (MDM2), can be regulated by APA-mediated inclusion/exclusion of duplex structures in the alternative 3' UTR. Indeed, depletion of master 3' UTR shortening regulators cleavage stimulation factor subunit 2 (CSTF2) and CSTF2 tau variant (CSTF2T) results in the lengthening of the 3' UTR of MDM2 and subsequent silencing of MDM2 protein expression through the inclusion of the duplex structures embedded in its alternative 3' UTR. More importantly, the downregulation of MDM2 by these duplex structures results in the phosphorylation of p53 and the activation of the p53 signaling pathway. Collectively, our work unveils the crosstalk between APA and endogenous dsRNAs in the post-transcriptional regulation of numerous biological processes including MDM2-p53 associated tumorigenesis.