Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins

Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins

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 (...

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Main Authors: Ji, Zhe, Song, Ruisheng, Regev, Aviv, Struhl, Kevin
Format: Online
Language:English
Published: eLife Sciences Publications, Ltd 2015
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4739776/
id pubmed-4739776
recordtype oai_dc
spelling pubmed-47397762016-02-05 Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins Ji, Zhe Song, Ruisheng Regev, Aviv Struhl, Kevin Cell Biology 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. eLife Sciences Publications, Ltd 2015-12-19 /pmc/articles/PMC4739776/ /pubmed/26687005 http://dx.doi.org/10.7554/eLife.08890 Text en © 2015, Ji et al http://creativecommons.org/licenses/by/4.0/ This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Ji, Zhe
Song, Ruisheng
Regev, Aviv
Struhl, Kevin
spellingShingle Ji, Zhe
Song, Ruisheng
Regev, Aviv
Struhl, Kevin
Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins
author_facet Ji, Zhe
Song, Ruisheng
Regev, Aviv
Struhl, Kevin
author_sort Ji, Zhe
title Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins
title_short Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins
title_full Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins
title_fullStr Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins
title_full_unstemmed Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins
title_sort many lncrnas, 5’utrs, and pseudogenes are translated and some are likely to express functional proteins
description 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.
publisher eLife Sciences Publications, Ltd
publishDate 2015
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4739776/
_version_ 1613533236421459968

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