The Poly(A)-Binding Protein Nuclear 1 Suppresses Alternative Cleavage and Polyadenylation Sites

Alternative cleavage and polyadenylation (APA) is emerging as an important layer of gene regulation. Factors controlling APA are largely unknown. We developed a reporter-based RNAi screen for APA and identified PABPN1 as a regulator of this process. Genome-wide analysis of APA in human cells showed that loss of PABPN1 resulted in extensive 3′ untranslated region shortening. Messenger RNA transcription, stability analyses, and in vitro cleavage assays indicated enhanced usage of proximal cleavage sites (CSs) as the underlying mechanism. Using Cyclin D1 as a test case, we demonstrated that enhanced usage of proximal CSs compromises microRNA-mediated repression. Triplet-repeat expansion in PABPN1 (trePABPN1) causes autosomal-dominant oculopharyngeal muscular dystrophy (OPMD). The expression of trePABPN1 in both a mouse model of OPMD and human cells elicited broad induction of proximal CS usage, linked to binding to endogenous PABPN1 and its sequestration in nuclear aggregates. Our results elucidate a novel function for PABPN1 as a suppressor of APA. [Display omitted] ▸ Genetic screen identifies PABPN1 as a regulator of alternative polyadenylation ▸ PABPN1 knockdown results in global 3′ UTR shortening ▸ Global 3′ UTR shortening is observed in an OPMD mouse model expressing mutant PABPN1 ▸ PABPN1 directly suppresses cleavage at proximal alternative 3′ UTRs The oculopharyngeal muscular dystrophy (OPMD) protein PABN1 regulates selection of alternative mRNA polyadenylation sites by binding to and suppressing the use of proximal sequences. Consequently, triplet-repeat expansion of the PABN1 gene in human OPMD results in widespread shortening of target mRNAs, contributing to pathogenesis of the disease.