Three periods of regulatory innovation during vertebrate evolution

Lowe, C. B., Kellis, M., Siepel, A., Raney, B. J., Clamp, M., Salama, S. R., Kingsley, D. M., Lindblad-Toh, K., Haussler, D. (2011) Three periods of regulatory innovation during vertebrate evolution. Science, 333 (6045). pp. 1019-24. ISSN 0036-8075

URL: http://www.ncbi.nlm.nih.gov/pubmed/21852499
DOI: 10.1126/science.1202702

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.

Item Type: Paper
Uncontrolled Keywords: Animals *Biological Evolution Cattle *Conserved Sequence DNA, Intergenic/genetics *Evolution, Molecular Gene Expression Regulation Genes, Developmental Genome Humans Markov Chains Mice Oryzias/genetics Phylogeny Protein Processing, Post-Translational/genetics *Regulatory Elements, Transcriptional *Regulatory Sequences, Nucleic Acid Selection, Genetic Sequence Alignment Smegmamorpha/genetics Transcription Factors/genetics Vertebrates/*genetics
Subjects: evolution
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene regulation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene regulation

bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
CSHL Authors:
Communities: CSHL labs > Siepel lab
Depositing User: Matt Covey
Date Deposited: 14 Jan 2015 15:41
Last Modified: 14 Jan 2015 15:41
PMCID: PMC3511857
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31080

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