MBE Advance Access published online on May 30, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg140
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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1 Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
* To whom correspondence should be addressed. E-mail: gwray{at}duke.edu.
Gene expression is central to the genotype:phenotype relationship in all organisms, and is an important component of the genetic basis for evolutionary change in diverse aspects of phenotype. However, the evolution of transcriptional regulation remains understudied and poorly understood. Here we review the evolutionary dynamics of promoter, or cis-regulatory, sequences, and the evolutionary mechanisms that shape these sequences. Existing evidence indicates that populations harbor extensive genetic variation in promoter sequences, that a substantial fraction of this variation has consequences for both biochemical and organismal phenotype, and that some of this functional variation is sorted by selection. As with protein-coding sequences, rates and patterns of promoter sequence evolution differ considerably among loci and among clades for reasons that are not well understood. Studying the evolution of transcriptional regulation poses empirical and conceptual challenges beyond those typically encountered in analyses of coding sequence evolution: promoter organization is much less regular than that of coding sequences, and sequences required for the transcription of each locus reside at multiple other loci in the genome. Sequence inspection alone provides limited information about promoter function due to the strong context-dependence of transcriptional regulation. Understanding the functional consequences of sequence differences among promoters generally requires biochemical and in vivo functional assays. Despite these challenges, important insights have already been gained into the evolution of transcriptional regulation, and the pace of discovery is accelerating. Key Words:
binding site, enhancer, evolution of development, genotype-phenotype relationship, promoter, transcription factor
© 2003 Society for Molecular Biology and Evolution
Review Article
The Evolution of Transcriptional Regulation in Eukaryotes
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|
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|
|
|
|
 |
|
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 |
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|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
D. A. Loisel, M. V. Rockman, G. A. Wray, J. Altmann, and S. C. Alberts Ancient polymorphism and functional variation in the primate MHC-DQA1 5' cis-regulatory region PNAS, October 31, 2006; 103(44): 16331 - 16336. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Sun, G. Skogerbo, and R. Chen Conserved distances between vertebrate highly conserved elements Hum. Mol. Genet., October 1, 2006; 15(19): 2911 - 2922. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
 G. A. Wray The evolution of embryonic gene expression in sea urchins Integr. Comp. Biol., June 1, 2006; 46(3): 233 - 242. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
A. Whitehead and D. L. Crawford Neutral and adaptive variation in gene expression PNAS, April 4, 2006; 103(14): 5425 - 5430. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. E. Vinogradov "Genome design" model: Evidence from conserved intronic sequence in human-mouse comparison Genome Res., March 1, 2006; 16(3): 347 - 354. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. J Stover Influence of human genetic variation on nutritional requirements Am. J. Clinical Nutrition, February 1, 2006; 83(2): 436S - 442S. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
E. A. D. Hammock and L. J. Young Microsatellite Instability Generates Diversity in Brain and Sociobehavioral Traits Science, June 10, 2005; 308(5728): 1630 - 1634. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
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J. Zhang, A. M. Dean, F. Brunet, and M. Long Evolving protein functional diversity in new genes of Drosophila PNAS, November 16, 2004; 101(46): 16246 - 16250. [Abstract] [Full Text] [PDF]
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 S. W. Pickrell, X. Zhu, X. Wang, and C. M. Craft Deciphering the Contribution of Known cis-Elements in the Mouse Cone Arrestin Gene to its Cone-Specific Expression Invest. Ophthalmol. Vis. Sci., November 1, 2004; 45(11): 3877 - 3884. [Abstract] [Full Text] [PDF]
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G. P. Wagner, C. Fried, S. J. Prohaska, and P. F. Stadler Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative Rate Tests Mol. Biol. Evol., November 1, 2004; 21(11): 2116 - 2121. [Abstract] [Full Text] [PDF]
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 S. M. Brugger, A. E. Merrill, J. Torres-Vazquez, N. Wu, M.-C. Ting, J. Y.-M. Cho, S. L. Dobias, S. E. Yi, K. Lyons, J. R. Bell, et al. A phylogenetically conserved cis-regulatory module in the Msx2 promoter is sufficient for BMP-dependent transcription in murine and Drosophila embryos Development, October 15, 2004; 131(20): 5153 - 5165. [Abstract] [Full Text] [PDF]
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G. Haberer, T. Hindemitt, B. C. Meyers, and K. F.X. Mayer Transcriptional Similarities, Dissimilarities, and Conservation of cis-Elements in Duplicated Genes of Arabidopsis Plant Physiology, October 1, 2004; 136(2): 3009 - 3022. [Abstract] [Full Text] [PDF]
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B. Snel, V. van Noort, and M. A. Huynen Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes Nucleic Acids Res., September 7, 2004; 32(16): 4725 - 4731. [Abstract] [Full Text] [PDF]
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