Translation of Small Open Reading Frames within Unannotated RNA Transcripts in Saccharomyces cerevisiae

Jenna E. Smith, Juan R. Alvarez-Dominguez, Nicholas Kline, Nathan J. Huynh, Sarah Geisler, Wenqian Hu, Jeff Coller, Kristian E. Baker

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90 Scopus citations

Abstract

High-throughput gene expression analysis has revealed a plethora of previously undetected transcripts in eukaryotic cells. In this study, we investigate <1,100 unannotated transcripts in yeast predicted to lack protein-coding capacity. We show that a majority of these RNAs are enriched on polyribosomes akin to mRNAs. Ribosome profiling demonstrates that many bind translocating ribosomes within predicted open reading frames 10-96 codons in size. We validate expression of peptides encoded within a subset of these RNAs and provide evidence for conservation among yeast species. Consistent with their translation, many of these transcripts are targeted for degradation by the translation-dependentnonsense-mediated RNA decay (NMD) pathway. We identify lncRNAs that are also sensitive to NMD, indicating that translation of noncoding transcripts also occurs in mammals. These data demonstrate transcripts considered to lack coding potential are bona fide protein coding and expand the proteome of yeast and possibly other eukaryotes.

Original languageEnglish (US)
Pages (from-to)1858-1866
Number of pages9
JournalCell reports
Volume7
Issue number6
DOIs
StatePublished - Jun 26 2014

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ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Smith, J. E., Alvarez-Dominguez, J. R., Kline, N., Huynh, N. J., Geisler, S., Hu, W., Coller, J., & Baker, K. E. (2014). Translation of Small Open Reading Frames within Unannotated RNA Transcripts in Saccharomyces cerevisiae. Cell reports, 7(6), 1858-1866. https://doi.org/10.1016/j.celrep.2014.05.023