A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation

• Published in: Genome research Vol. 26; no. 8; pp. 1145 - 1159
• Main Authors: Gruber, Andreas J, Schmidt, Ralf, Gruber, Andreas R, Martin, Georges, Ghosh, Souvik, Belmadani, Manuel, Keller, Walter, Zavolan, Mihaela
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01-08-2016
• Subjects: 3' Untranslated Regions - genetics; Animals; Binding Sites; Cytoplasm - genetics; Gene Expression; Heterogeneous-Nuclear Ribonucleoprotein Group C - genetics; Humans; Mice; Polyadenylation - genetics; Resource; RNA, Messenger - genetics; RNA-Binding Proteins - genetics; Transcription, Genetic
• ISSN: 1088-9051; 1549-5469
• DOI: 10.1101/gr.202432.115

Alternative polyadenylation (APA) is a general mechanism of transcript diversification in mammals, which has been recently linked to proliferative states and cancer. Different 3' untranslated region (3' UTR) isoforms interact with different RNA-binding proteins (RBPs), which modify the stability, translation, and subcellular localization of the corresponding transcripts. Although the heterogeneity of pre-mRNA 3' end processing has been established with high-throughput approaches, the mechanisms that underlie systematic changes in 3' UTR lengths remain to be characterized. Through a uniform analysis of a large number of 3' end sequencing data sets, we have uncovered 18 signals, six of which are novel, whose positioning with respect to pre-mRNA cleavage sites indicates a role in pre-mRNA 3' end processing in both mouse and human. With 3' end sequencing we have demonstrated that the heterogeneous ribonucleoprotein C (HNRNPC), which binds the poly(U) motif whose frequency also peaks in the vicinity of polyadenylation (poly(A)) sites, has a genome-wide effect on poly(A) site usage. HNRNPC-regulated 3' UTRs are enriched in ELAV-like RBP 1 (ELAVL1) binding sites and include those of the CD47 gene, which participate in the recently discovered mechanism of 3' UTR-dependent protein localization (UDPL). Our study thus establishes an up-to-date, high-confidence catalog of 3' end processing sites and poly(A) signals, and it uncovers an important role of HNRNPC in regulating 3' end processing. It further suggests that U-rich elements mediate interactions with multiple RBPs that regulate different stages in a transcript's life cycle.