Publication Date:
2011-08-20
Description:
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.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511857/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511857/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lowe, Craig B -- Kellis, Manolis -- Siepel, Adam -- Raney, Brian J -- Clamp, Michele -- Salama, Sofie R -- Kingsley, David M -- Lindblad-Toh, Kerstin -- Haussler, David -- 1U01-HG004695/HG/NHGRI NIH HHS/ -- 5P41-HG002371/HG/NHGRI NIH HHS/ -- P41 HG002371/HG/NHGRI NIH HHS/ -- P50 HG002568/HG/NHGRI NIH HHS/ -- P50-HG02568/HG/NHGRI NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01-HG004037/HG/NHGRI NIH HHS/ -- U01 HG004695/HG/NHGRI NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- U54-HG003067/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Aug 19;333(6045):1019-24. doi: 10.1126/science.1202702.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21852499" target="_blank"〉PubMed〈/a〉
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
Print ISSN:
0036-8075
Electronic ISSN:
1095-9203
Topics:
Biology
,
Chemistry and Pharmacology
,
Computer Science
,
Medicine
,
Natural Sciences in General
,
Physics
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