Lowe, C. B., Kellis, M., Siepel, A., Raney, B. J., Clamp, M., Salama, S. R., Kingsley, D. M., Lindblad-Toh, K., Haussler, D.
(August 2011)
Three periods of regulatory innovation during vertebrate evolution.
Science, 333 (6045).
pp. 1019-24.
ISSN 0036-8075
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: |
19 August 2011 |
| Date Deposited: |
14 Jan 2015 15:41 |
| Last Modified: |
02 Oct 2019 15:26 |
| PMCID: |
PMC3511857 |
| Related URLs: |
|
| URI: |
https://repository.cshl.edu/id/eprint/31080 |
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