Three Periods of Regulatory Innovation During Vertebrate Evolution
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Kellis_Three periods.pdf
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Author(s)
Kellis, Manolis
Lowe, Craig B.
Siepel, Adam
Raney, Brian J.
Clamp, Michele
Salama, Sofie R.
Kingsley, David M.
Lindblad-Toh, Kerstin
Haussler, David
Date Issued
August 2011
Journal
Science
Publisher
American Association for the Advancement of Science (AAAS)
Citation
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.
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Author's final manuscript
Abstract
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.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
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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.
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DOI of Published Version
https://doi.org/10.1126/science.1202702
