Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells
About Evangelos Karousis
Evangelos Karousis is a senior researcher and lecturer at the Department of Chemistry and Biochemistry, University of Bern, Switzerland. He is interested in post-transcriptional mRNA regulation in mammalian cells and applies nanopore sequencing to identify endogenous mRNAs that are sensitive to nonsense-mediated mRNA decay. He is a biochemist from Greece with a background in transcriptomics, RNA decay, and in vitro translation.
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. To identify and analyse endogenous targets of NMD, we applied cDNA nanopore sequencing and short-read sequencing to human cells with varying expression levels of NMD factors. Long-read sequencing enabled the identification of many novel NMD-sensitive mRNAs and revealed 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.