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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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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eLife Sciences Publications, Ltd.
2016
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| Online Access: | http://hdl.handle.net/1721.1/101022 https://orcid.org/0000-0001-8567-2049 |
| _version_ | 1811090282380263424 |
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| author | Ji, Zhe Song, Ruisheng Regev, Aviv Struhl, Kevin |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Ji, Zhe Song, Ruisheng Regev, Aviv Struhl, Kevin |
| author_sort | Ji, Zhe |
| collection | MIT |
| 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 | 2024-09-23T14:40:52Z |
| format | Article |
| id | mit-1721.1/101022 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T14:40:52Z |
| publishDate | 2016 |
| publisher | eLife Sciences Publications, Ltd. |
| record_format | dspace |
| spelling | mit-1721.1/1010222022-10-01T22:03:06Z Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins Ji, Zhe Song, Ruisheng Regev, Aviv Struhl, Kevin Massachusetts Institute of Technology. Department of Biology Regev, Aviv 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. 2016-01-28T02:43:08Z 2016-01-28T02:43:08Z 2015-12 2015-05 Article http://purl.org/eprint/type/JournalArticle 2050-084X http://hdl.handle.net/1721.1/101022 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). https://orcid.org/0000-0001-8567-2049 en_US http://dx.doi.org/10.7554/eLife.08890 eLife Creative Commons Attribution http://creativecommons.org/licenses/by/4.0/ application/pdf eLife Sciences Publications, Ltd. eLife Sciences Publications, Ltd. |
| 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 |
| 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 |
| url | http://hdl.handle.net/1721.1/101022 https://orcid.org/0000-0001-8567-2049 |
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