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Three periods of regulatory innovation during vertebrate evolution.

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Date
2011-08
Authors
Lowe, Craig B
Kellis, Manolis
Siepel, Adam
Raney, Brian J
Clamp, Michele
Salama, Sofie R
Kingsley, David M
Lindblad-Toh, Kerstin
Haussler, David
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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.
Type
Journal article
Subject
Animals
Vertebrates
Smegmamorpha
Oryzias
Cattle
Humans
Mice
Transcription Factors
DNA, Intergenic
Markov Chains
Sequence Alignment
Evolution, Molecular
Phylogeny
Gene Expression Regulation
Protein Processing, Post-Translational
Regulatory Sequences, Nucleic Acid
Conserved Sequence
Genome
Regulatory Elements, Transcriptional
Genes, Developmental
Selection, Genetic
Biological Evolution
Permalink
https://hdl.handle.net/10161/17403
Published Version (Please cite this version)
10.1126/science.1202702
Publication Info
Lowe, Craig B; Kellis, Manolis; Siepel, Adam; Raney, Brian J; Clamp, Michele; Salama, Sofie R; ... Haussler, David (2011). Three periods of regulatory innovation during vertebrate evolution. Science (New York, N.Y.), 333(6045). pp. 1019-1024. 10.1126/science.1202702. Retrieved from https://hdl.handle.net/10161/17403.
This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.
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Scholars@Duke

Lowe

Craig Lowe

Assistant Professor of Molecular Genetics and Microbiology
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