Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells

Karousis, Evangelos D.; Gypas, Foivos; Zavolan, Mihaela; Mühlemann, Oliver (2021). Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells. Genome biology, 22(1), p. 223. BioMed Central Ltd. 10.1186/s13059-021-02439-3

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Background: Nonsense-mediated mRNA decay (NMD) is a eukaryotic, translation-dependent degradation pathway that targets mRNAs with premature termination codons and also regulates the expression of some mRNAs that encode full-length proteins. Although many genes express NMD-sensitive transcripts, identifying them based on short-read sequencing data remains a challenge.

Results: To identify and analyze endogenous targets of NMD, we apply cDNA Nanopore sequencing and short-read sequencing to human cells with varying expression levels of NMD factors. Our approach detects full-length NMD substrates that are highly unstable and increase in levels or even only appear when NMD is inhibited. Among the many new NMD-targeted isoforms that our analysis identifies, most derive from alternative exon usage. The isoform-aware analysis reveals many genes with significant changes in splicing but no significant changes in overall expression levels upon NMD knockdown. NMD-sensitive mRNAs have more exons in the 3΄UTR and, for those mRNAs with a termination codon in the last exon, the length of the 3΄UTR per se does not correlate with NMD sensitivity. Analysis of splicing signals reveals isoforms where NMD has been co-opted in the regulation of gene expression, though the main function of NMD seems to be ridding the transcriptome of isoforms resulting from spurious splicing events.

Conclusions: Long-read sequencing enables the identification of many novel NMD-sensitive mRNAs and reveals both known and unexpected features concerning their biogenesis and their biological role. Our data provide a highly valuable resource of human NMD transcript targets for future genomic and transcriptomic applications.

Keywords: Long-read sequencing; NMD; Nanopore sequencing; Nonsense-mediated mRNA decay; cDNA sequencing; mRNA degradation; mRNA isoforms; transcriptomics.

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP)

UniBE Contributor:

Karousis, Evangelos, Mühlemann, Oliver


500 Science > 570 Life sciences; biology
500 Science > 540 Chemistry




BioMed Central Ltd.




Christina Schüpbach

Date Deposited:

14 Oct 2021 15:28

Last Modified:

29 Mar 2023 22:39

Publisher DOI:


PubMed ID:





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