Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways

RNA. 2017 Feb;23(2):189-201. doi: 10.1261/rna.059055.116. Epub 2016 Nov 18.


Besides degrading aberrant mRNAs that harbor a premature translation termination codon (PTC), nonsense-mediated mRNA decay (NMD) also targets many seemingly "normal" mRNAs that encode for full-length proteins. To identify a bona fide set of such endogenous NMD targets in human cells, we applied a meta-analysis approach in which we combined transcriptome profiling of knockdowns and rescues of the three NMD factors UPF1, SMG6, and SMG7. We provide evidence that this combinatorial approach identifies NMD-targeted transcripts more reliably than previous attempts that focused on inactivation of single NMD factors. Our data revealed that SMG6 and SMG7 act on essentially the same transcripts, indicating extensive redundancy between the endo- and exonucleolytic decay routes. Besides mRNAs, we also identified as NMD targets many long noncoding RNAs as well as miRNA and snoRNA host genes. The NMD target feature with the most predictive value is an intron in the 3' UTR, followed by the presence of upstream open reading frames (uORFs) and long 3' UTRs. Furthermore, the 3' UTRs of NMD-targeted transcripts tend to have an increased GC content and to be phylogenetically less conserved when compared to 3' UTRs of NMD insensitive transcripts.

Keywords: RNA turnover; SMG6; SMG7; UPF1; bioinformatics analysis; mRNA-seq; nonsense-mediated mRNA decay; post-transcriptional gene regulation.

MeSH terms

  • Base Composition
  • Carrier Proteins / antagonists & inhibitors
  • Carrier Proteins / genetics
  • Carrier Proteins / metabolism*
  • Codon, Nonsense
  • Gene Expression
  • HeLa Cells
  • Humans
  • Introns
  • MicroRNAs / chemistry
  • MicroRNAs / metabolism
  • Nonsense Mediated mRNA Decay*
  • Protein Binding
  • RNA Helicases
  • RNA, Long Noncoding / chemistry
  • RNA, Long Noncoding / metabolism
  • RNA, Messenger / chemistry
  • RNA, Messenger / metabolism*
  • RNA, Small Interfering / genetics
  • RNA, Small Interfering / metabolism
  • RNA, Small Nucleolar / chemistry
  • RNA, Small Nucleolar / metabolism
  • Telomerase / antagonists & inhibitors
  • Telomerase / genetics
  • Telomerase / metabolism*
  • Trans-Activators / antagonists & inhibitors
  • Trans-Activators / genetics
  • Trans-Activators / metabolism*
  • Transcriptome*


  • Carrier Proteins
  • Codon, Nonsense
  • MicroRNAs
  • RNA, Long Noncoding
  • RNA, Messenger
  • RNA, Small Interfering
  • RNA, Small Nucleolar
  • SMG7 protein, human
  • Trans-Activators
  • Telomerase
  • SMG6 protein, human
  • RNA Helicases
  • UPF1 protein, human