Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins
Name
Ji-2015-Many IncRNAs.pdf
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2.69 MB
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Adobe PDF
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Author(s)
Ji, Zhe
Song, Ruisheng
Regev, Aviv
Struhl, Kevin
Date Issued
December 2015
Journal
eLife
Publisher
eLife Sciences Publications, Ltd.
Citation
Ji, Zhe, Ruisheng Song, Aviv Regev, and Kevin Struhl. “Many lncRNAs, 5’UTRs, and Pseudogenes Are Translated and Some Are Likely to Express Functional Proteins.” eLife 4 (December 19, 2015).
Version
Final published version
Abstract
Using a new bioinformatic method to analyze ribosome profiling data, we show that 40% of lncRNAs and pseudogene RNAs expressed in human cells are translated. In addition, ~35% of mRNA coding genes are translated upstream of the primary protein-coding region (uORFs) and 4% are translated downstream (dORFs). Translated lncRNAs preferentially localize in the cytoplasm, whereas untranslated lncRNAs preferentially localize in the nucleus. The translation efficiency of cytoplasmic lncRNAs is nearly comparable to that of mRNAs, suggesting that cytoplasmic lncRNAs are engaged by the ribosome and translated. While most peptides generated from lncRNAs may be highly unstable byproducts without function, ~9% of the peptides are conserved in ORFs in mouse transcripts, as are 74% of pseudogene peptides, 24% of uORF peptides and 32% of dORF peptides. Analyses of synonymous and nonsynonymous substitution rates of these conserved peptides show that some are under stabilizing selection, suggesting potential functional importance.
MIT Department
Massachusetts Institute of Technology. Department of Biology
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.7554/eLife.08890
