UMMS Affiliation

Department of Microbiology and Physiological Systems

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Document Type



Bioinformatics | Computational Biology | Genetics and Genomics | Microbiology


Nonsense-mediated mRNA decay (NMD) plays an important role in eukaryotic gene expression, yet the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we reevaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. Our new RNA-seq analyses confirm previous results of microarray studies, but also uncover hundreds of new NMD-regulated transcripts that had escaped previous detection, including many intron-containing pre-mRNAs and several noncoding RNAs. The vast majority of NMD-regulated transcripts are normal-looking protein-coding mRNAs. Our bioinformatics analyses reveal that this set of NMD-regulated transcripts generally have lower translational efficiency and higher ratios of out-of-frame translation. NMD-regulated transcripts also have lower average codon optimality scores and higher transition probability to nonoptimal codons. Collectively, our results generate a comprehensive catalog of yeast NMD substrates and yield new insights into the mechanisms by which these transcripts are targeted by NMD.


NMD substrates, codon optimality, translational fidelity and efficiency

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Copyright © 2017 Celik et al.

DOI of Published Version



RNA. 2017 May;23(5):735-748. doi: 10.1261/rna.060541.116. Epub 2017 Feb 16. Link to article on publisher's site

Journal/Book/Conference Title

RNA (New York, N.Y.)

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PubMed ID


Creative Commons License

Creative Commons Attribution-Noncommercial 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License