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    Three periods of regulatory innovation during vertebrate evolution.

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    Date
    2011-08
    Authors
    Lowe, Craig
    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; 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
    Open Access

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