Evolution of cis-regulatory sequence and function in Diptera

Wittkopp, Patricia J.

doi:10.1038/sj.hdy.6800869

Cited by 57 publications

(41 citation statements)

References 102 publications

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“…Consistent with previous findings, Drosophila cis-regulatory sequences are highly constrained 148,149 . Mean constraint within cisregulatory modules is 0.643 (95% bootstrap confidence interval 5 0.621-0.662) and within footprints is 0.692 (0.655-0.723), both of which are significantly higher than mean constraint in non-coding DNA overall (0.555 (0.546-0.563)) and significantly lower than constraint at non-degenerate coding sites (0.862 (0.856-0.868)) and ncRNA genes (0.864 (0.846-0.880)) (Supplementary Fig.…”

Section: Articlessupporting

confidence: 80%

Evolution of genes and genomes on the Drosophila phylogeny

Clark¹,

Eisen²,

Smith³

et al. 2007

Nature

1,816

1,041

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Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

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Section: Articlessupporting

confidence: 80%

Evolution of genes and genomes on the Drosophila phylogeny

Clark¹,

Eisen²,

Smith³

et al. 2007

Nature

1,816

1,041

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“…For example, changes in gene expression, especially between species, are often caused by divergent cis-regulatory sequences (Brem et al, 2002;Yan et al, 2002;Schadt et al, 2003;Wittkopp et al, 2004), which are not well understood. The uncoupling of cis-regulatory sequence and function limits our ability to predict the phenotypic consequences of individual base substitutions (Tautz, 2000;Wittkopp, 2006). However, detailed studies of cis-regulatory regions are in progress for many model systems, including humans (ENCODE, 2004).…”

Section: Discussionmentioning

confidence: 99%

Evaluating the role of natural selection in the evolution of gene regulation

Fay¹,

2007

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Surveys of gene expression reveal extensive variability both within and between a wide range of species. Compelling cases have been made for adaptive changes in gene regulation, but the proportion of expression divergence attributable to natural selection remains unclear. Distinguishing adaptive changes driven by positive selection from neutral divergence resulting from mutation and genetic drift is critical for understanding the evolution of gene expression. Here, we review the various methods that have been used to test for signs of selection in genomic expression data. We also discuss properties of regulatory systems relevant to neutral models of gene expression. Despite some potential caveats, published studies provide considerable evidence for adaptive changes in gene expression. Future challenges for studies of regulatory evolution will be to quantify the frequency of adaptive changes, identify the genetic basis of expression divergence and associate changes in gene expression with specific organismal phenotypes.

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“…Because coding sequences are usually sufficiently conserved to identify orthologous sequences among different phyla, it was naïvely assumed initially that the same would hold true for CREs, and that functional comparison of divergent CREs from distantly related taxa would be possible. However, it was progressively realized that the turnover rate of noncoding DNA is much higher than for coding sequences, largely because of looser functional constraints, making orthologous sequence identification and comparison much more difficult (23)(24)(25) and often impossible, especially among higher arthropod taxa. To circumvent this difficulty, an alternative strategy has been to focus on rapidly evolving traits among closely related species or populations.…”

mentioning

confidence: 99%

Emerging principles of regulatory evolution

Prud’homme

Gompel

Carroll

2007

Proc. Natl. Acad. Sci. U.S.A.

481

437

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Understanding the genetic and molecular mechanisms governing the evolution of morphology is a major challenge in biology. Because most animals share a conserved repertoire of body-building and -patterning genes, morphological diversity appears to evolve primarily through changes in the deployment of these genes during development. The complex expression patterns of developmentally regulated genes are typically controlled by numerous independent cis-regulatory elements (CREs). It has been proposed that morphological evolution relies predominantly on changes in the architecture of gene regulatory networks and in particular on functional changes within CREs. Here, we discuss recent experimental studies that support this hypothesis and reveal some unanticipated features of how regulatory evolution occurs. From this growing body of evidence, we identify three key operating principles underlying regulatory evolution, that is, how regulatory evolution: (i) uses available genetic components in the form of preexisting and active transcription factors and CREs to generate novelty; (ii) minimizes the penalty to overall fitness by introducing discrete changes in gene expression; and (iii) allows interactions to arise among any transcription factor and downstream CRE. These principles endow regulatory evolution with a vast creative potential that accounts for both relatively modest morphological differences among closely related species and more profound anatomical divergences among groups at higher taxonomical levels.pleiotropy ͉ cis-regulation ͉ transcription ͉ pigmentation ͉ body plan

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Evolution of cis-regulatory sequence and function in Diptera

Cited by 57 publications

References 102 publications

Evolution of genes and genomes on the Drosophila phylogeny

Evolution of genes and genomes on the Drosophila phylogeny

Evaluating the role of natural selection in the evolution of gene regulation

Emerging principles of regulatory evolution

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