UMMS Affiliation

Department of Microbiology and Physiological Systems

Date

5-1-2017

Document Type

Article

Disciplines

Bioinformatics | Computational Biology | Genetics and Genomics | Microbiology

Abstract

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.

Rights and Permissions

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

DOI of Published Version

10.1261/rna.060541.116

Related Resources

Link to Article in PubMed

Keywords

NMD substrates, codon optimality, translational fidelity and efficiency

Journal Title

RNA (New York, N.Y.)

PubMed ID

28209632

Creative Commons License

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

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