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Activation and inhibition of nonsense-mediated mRNA decay control the abundance of alternative polyadenylation products.

Research paper by Aparna A Kishor, Sarah E SE Fritz, Nazmul N Haque, Zhiyun Z Ge, Ilker I Tunc, Wenjing W Yang, Jun J Zhu, J Robert JR Hogg

Indexed on: 18 Jun '20Published on: 17 Jun '20Published in: Nucleic acids research



Abstract

Alternative polyadenylation (APA) produces transcript 3' untranslated regions (3'UTRs) with distinct sequences, lengths, stabilities and functions. We show here that APA products include a class of cryptic nonsense-mediated mRNA decay (NMD) substrates with extended 3'UTRs that gene- or transcript-level analyses of NMD often fail to detect. Transcriptome-wide, the core NMD factor UPF1 preferentially recognizes long 3'UTR products of APA, leading to their systematic downregulation. Counteracting this mechanism, the multifunctional RNA-binding protein PTBP1 regulates the balance of short and long 3'UTR isoforms by inhibiting NMD, in addition to its previously described modulation of co-transcriptional polyadenylation (polyA) site choice. Further, we find that many transcripts with altered APA isoform abundance across multiple tumor types are controlled by NMD. Together, our findings reveal a widespread role for NMD in shaping the outcomes of APA. Published by Oxford University Press on behalf of Nucleic Acids Research 2020.