Three Periods of Regulatory Innovation During Vertebrate Evolution
The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebra...
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| Materiálatiipa: | Artihkal |
| Giella: | en_US |
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American Association for the Advancement of Science (AAAS)
2014
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| Liŋkkat: | http://hdl.handle.net/1721.1/87017 |
| _version_ | 1826209282353266688 |
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| author | Kellis, Manolis Lowe, Craig B. Siepel, Adam Raney, Brian J. Clamp, Michele Salama, Sofie R. Kingsley, David M. Lindblad-Toh, Kerstin Haussler, David |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Kellis, Manolis Lowe, Craig B. Siepel, Adam Raney, Brian J. Clamp, Michele Salama, Sofie R. Kingsley, David M. Lindblad-Toh, Kerstin Haussler, David |
| author_sort | Kellis, Manolis |
| collection | MIT |
| description | The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory regions are conserved nonexonic elements (CNEEs), which are evolutionarily conserved yet do not overlap any coding or noncoding mature transcript. We then inferred the branch on which each CNEE came under selective constraint. Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers. |
| first_indexed | 2024-09-23T14:20:03Z |
| format | Article |
| id | mit-1721.1/87017 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T14:20:03Z |
| publishDate | 2014 |
| publisher | American Association for the Advancement of Science (AAAS) |
| record_format | dspace |
| spelling | mit-1721.1/870172022-09-29T08:46:29Z Three Periods of Regulatory Innovation During Vertebrate Evolution Kellis, Manolis Lowe, Craig B. Siepel, Adam Raney, Brian J. Clamp, Michele Salama, Sofie R. Kingsley, David M. Lindblad-Toh, Kerstin Haussler, David Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Kellis, Manolis The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory regions are conserved nonexonic elements (CNEEs), which are evolutionarily conserved yet do not overlap any coding or noncoding mature transcript. We then inferred the branch on which each CNEE came under selective constraint. Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers. National Science Foundation (U.S.) (CAREER-0644282) National Institutes of Health (U.S.) (R01-HG004037) Alfred P. Sloan Foundation 2014-05-15T19:40:28Z 2014-05-15T19:40:28Z 2011-08 2011-01 Article http://purl.org/eprint/type/JournalArticle 0036-8075 1095-9203 http://hdl.handle.net/1721.1/87017 Lowe, C. B., M. Kellis, A. Siepel, B. J. Raney, M. Clamp, S. R. Salama, D. M. Kingsley, K. Lindblad-Toh, and D. Haussler. “Three Periods of Regulatory Innovation During Vertebrate Evolution.” Science 333, no. 6045 (August 19, 2011): 1019–1024. en_US http://dx.doi.org/10.1126/science.1202702 Science Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf American Association for the Advancement of Science (AAAS) PMC |
| spellingShingle | Kellis, Manolis Lowe, Craig B. Siepel, Adam Raney, Brian J. Clamp, Michele Salama, Sofie R. Kingsley, David M. Lindblad-Toh, Kerstin Haussler, David Three Periods of Regulatory Innovation During Vertebrate Evolution |
| title | Three Periods of Regulatory Innovation During Vertebrate Evolution |
| title_full | Three Periods of Regulatory Innovation During Vertebrate Evolution |
| title_fullStr | Three Periods of Regulatory Innovation During Vertebrate Evolution |
| title_full_unstemmed | Three Periods of Regulatory Innovation During Vertebrate Evolution |
| title_short | Three Periods of Regulatory Innovation During Vertebrate Evolution |
| title_sort | three periods of regulatory innovation during vertebrate evolution |
| url | http://hdl.handle.net/1721.1/87017 |
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