Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways
- Martino Colombo1,2,3,
- Evangelos D. Karousis1,
- Joël Bourquin1,4,
- Rémy Bruggmann2 and
- Oliver Mühlemann1
- 1Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
- 2Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, CH-3012 Bern, Switzerland
- 3Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
- Corresponding author: oliver.muehlemann{at}dcb.unibe.ch
Abstract
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
- nonsense-mediated mRNA decay
- RNA turnover
- post-transcriptional gene regulation
- mRNA-seq
- UPF1
- SMG6
- SMG7
- bioinformatics analysis
Footnotes
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Article is online at http://www.rnajournal.org/cgi/doi/10.1261/rna.059055.116.
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Freely available online through the RNA Open Access option.
- Received September 2, 2016.
- Accepted November 5, 2016.
This article, published in RNA, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.