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 (...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2015-12-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/08890 |
| _version_ | 1818019091665911808 |
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| author | Zhe Ji Ruisheng Song Aviv Regev Kevin Struhl |
| author_facet | Zhe Ji Ruisheng Song Aviv Regev Kevin Struhl |
| author_sort | Zhe Ji |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-14T07:46:55Z |
| format | Article |
| id | doaj.art-34c825865e8c4c33b2f87ba73e41549b |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-14T07:46:55Z |
| publishDate | 2015-12-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-34c825865e8c4c33b2f87ba73e41549b2022-12-22T02:05:18ZengeLife Sciences Publications LtdeLife2050-084X2015-12-01410.7554/eLife.08890Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteinsZhe Ji0Ruisheng Song1https://orcid.org/0000-0002-6856-4721Aviv Regev2Kevin Struhl3Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States; Broad Institute of MIT and Harvard, Cambridge, United StatesDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United StatesBroad Institute of MIT and Harvard, Cambridge, United States; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United StatesDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United StatesUsing 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.https://elifesciences.org/articles/08890non-coding RNAtranslationribosome profiling5'UTRpseudogenebiological function |
| spellingShingle | Zhe Ji Ruisheng Song Aviv Regev Kevin Struhl Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins eLife non-coding RNA translation ribosome profiling 5'UTR pseudogene biological function |
| title | 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_short | 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 |
| topic | non-coding RNA translation ribosome profiling 5'UTR pseudogene biological function |
| url | https://elifesciences.org/articles/08890 |
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