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RNA. 2017 Aug;23(8):1224-1236. doi: 10.1261/rna.059659.116. Epub 2017 May 1.

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

Author information

1
Institute for Genetics, University of Cologne, 50674 Cologne, Germany.
2
Division of Brain Sciences, Imperial College London, London W12 0NN, United Kingdom.
3
Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom.

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.

KEYWORDS:

NMD; SMG6; SMG7; decay intermediates; degradome sequencing; endonucleolytic cleavage

PMID:
28461625
PMCID:
PMC5513067
DOI:
10.1261/rna.059659.116
[Indexed for MEDLINE]
Free PMC Article

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