Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species
The inability to predict long noncoding RNAs from genomic sequence has impeded the use of comparative genomics for studying their biology. Here, we develop methods that use RNA sequencing (RNA-seq) data to annotate the transcriptomes of 16 vertebrates and the echinoid sea urchin, uncovering thousand...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | en_US |
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Elsevier
2016
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| Online Access: | http://hdl.handle.net/1721.1/101429 https://orcid.org/0000-0002-3872-2856 |
| _version_ | 1826198609851318272 |
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| author | Hezroni, Hadas Koppstein, David Schwartz, Matthew G. Avrutin, Alexandra Ulitsky, Igor Bartel, David |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Hezroni, Hadas Koppstein, David Schwartz, Matthew G. Avrutin, Alexandra Ulitsky, Igor Bartel, David |
| author_sort | Hezroni, Hadas |
| collection | MIT |
| description | The inability to predict long noncoding RNAs from genomic sequence has impeded the use of comparative genomics for studying their biology. Here, we develop methods that use RNA sequencing (RNA-seq) data to annotate the transcriptomes of 16 vertebrates and the echinoid sea urchin, uncovering thousands of previously unannotated genes, most of which produce long intervening noncoding RNAs (lincRNAs). Although in each species, >70% of lincRNAs cannot be traced to homologs in species that diverged >50 million years ago, thousands of human lincRNAs have homologs with similar expression patterns in other species. These homologs share short, 5′-biased patches of sequence conservation nested in exonic architectures that have been extensively rewired, in part by transposable element exonization. Thus, over a thousand human lincRNAs are likely to have conserved functions in mammals, and hundreds beyond mammals, but those functions require only short patches of specific sequences and can tolerate major changes in gene architecture. |
| first_indexed | 2024-09-23T11:07:28Z |
| format | Article |
| id | mit-1721.1/101429 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T11:07:28Z |
| publishDate | 2016 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | mit-1721.1/1014292022-09-27T17:19:05Z Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species Hezroni, Hadas Koppstein, David Schwartz, Matthew G. Avrutin, Alexandra Ulitsky, Igor Bartel, David Massachusetts Institute of Technology. Department of Biology Whitehead Institute for Biomedical Research Bartel, David The inability to predict long noncoding RNAs from genomic sequence has impeded the use of comparative genomics for studying their biology. Here, we develop methods that use RNA sequencing (RNA-seq) data to annotate the transcriptomes of 16 vertebrates and the echinoid sea urchin, uncovering thousands of previously unannotated genes, most of which produce long intervening noncoding RNAs (lincRNAs). Although in each species, >70% of lincRNAs cannot be traced to homologs in species that diverged >50 million years ago, thousands of human lincRNAs have homologs with similar expression patterns in other species. These homologs share short, 5′-biased patches of sequence conservation nested in exonic architectures that have been extensively rewired, in part by transposable element exonization. Thus, over a thousand human lincRNAs are likely to have conserved functions in mammals, and hundreds beyond mammals, but those functions require only short patches of specific sequences and can tolerate major changes in gene architecture. National Institutes of Health (U.S.) (GM067031) 2016-03-03T02:55:49Z 2016-03-03T02:55:49Z 2015-05 Article http://purl.org/eprint/type/JournalArticle 22111247 http://hdl.handle.net/1721.1/101429 Hezroni, Hadas, David Koppstein, Matthew G. Schwartz, Alexandra Avrutin, David P. Bartel, and Igor Ulitsky. “Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species.” Cell Reports 11, no. 7 (May 2015): 1110–1122. https://orcid.org/0000-0002-3872-2856 en_US http://dx.doi.org/10.1016/j.celrep.2015.04.023 Cell Reports Creative Commons Attribution http://creativecommons.org/licenses/by-nc-nd/4.0/ application/pdf Elsevier Elsevier |
| spellingShingle | Hezroni, Hadas Koppstein, David Schwartz, Matthew G. Avrutin, Alexandra Ulitsky, Igor Bartel, David Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species |
| title | Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species |
| title_full | Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species |
| title_fullStr | Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species |
| title_full_unstemmed | Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species |
| title_short | Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species |
| title_sort | principles of long noncoding rna evolution derived from direct comparison of transcriptomes in 17 species |
| url | http://hdl.handle.net/1721.1/101429 https://orcid.org/0000-0002-3872-2856 |
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