Transcript-specific characteristics determine the contribution of endo- and exonucleolytic decay pathways during the degradation of nonsense-mediated decay substrates

Franziska Ottens, Volker Boehm, Christopher R Sibley, Jernej Ule, Niels H Gehring

Research output: Contribution to journalArticlepeer-review

Abstract

Nonsense-mediated mRNA decay (NMD) controls gene expression by eliminating mRNAs with premature or aberrant translation termination. Degradation of NMD substrates is initiated by the central NMD factor UPF1, which recruits the endonuclease SMG6 and the deadenylation-promoting SMG5/7 complex. The extent to which SMG5/7 and SMG6 contribute to the degradation of individual substrates and their regulation by UPF1 remains elusive. Here we map transcriptome-wide sites of SMG6-mediated endocleavage via 3' fragment capture and degradome sequencing. This reveals that endogenous transcripts can have NMD-eliciting features at various positions, including upstream open reading frames (uORFs), premature termination codons (PTCs), and long 3' UTRs. We find that NMD substrates with PTCs undergo constitutive SMG6-dependent endocleavage, rather than SMG7-dependent exonucleolytic decay. In contrast, the turnover of NMD substrates containing uORFs and long 3' UTRs involves both SMG6- and SMG7-dependent endo- and exonucleolytic decay, respectively. This suggests that the extent to which SMG6 and SMG7 degrade NMD substrates is determined by the mRNA architecture.

Original languageEnglish
Pages (from-to)1224-1236
Number of pages13
JournalRNA
Volume23
Issue number8
Early online date1 May 2017
DOIs
Publication statusE-pub ahead of print - 1 May 2017

Keywords

  • Carrier Proteins/genetics
  • Codon, Nonsense
  • HeLa Cells
  • Humans
  • Nonsense Mediated mRNA Decay
  • Open Reading Frames
  • RNA Helicases
  • RNA, Messenger/genetics
  • Telomerase/genetics
  • Trans-Activators/genetics

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