Evidence for stabilizing selection in a eukaryotic enhancer element. Nature

Department of Ecology and Evolution, University of Chicago, Illinois 60637, USA.
Nature (Impact Factor: 41.46). 03/2000; 403(6769):564-7. DOI: 10.1038/35000615
Source: PubMed


Eukaryotic gene expression is mediated by compact cis-regulatory modules, or enhancers, which are bound by specific sets of transcription factors. The combinatorial interaction of these bound transcription factors determines time- and tissue-specific gene activation or repression. The even-skipped stripe 2 element controls the expression of the second transverse stripe of even-skipped messenger RNA in Drosophila melanogaster embryos, and is one of the best characterized eukaryotic enhancers. Although even-skipped stripe 2 expression is strongly conserved in Drosophila, the stripe 2 element itself has undergone considerable evolutionary change in its binding-site sequences and the spacing between them. We have investigated this apparent contradiction, and here we show that two chimaeric enhancers, constructed by swapping the 5' and 3' halves of the native stripe 2 elements of two species, no longer drive expression of a reporter gene in the wildtype pattern. Sequence differences between species have functional consequences, therefore, but they are masked by other co-evolved differences. On the basis of these results, we present a model for the evolution of eukaryotic regulatory sequences.

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    • "Another model, the McDonald–Kreitman test, considers polymorphisms within a species and substitutions between species (McDonald and Kreitman 1991) and has been used to assess TF binding site gains and losses in Drosophila (He, Holloway, et al. 2011), and was also applied to all human TFs with ENCODE ChIP-Seq data (Arbiza et al. 2013). Although studying turnover of individual TF binding sites can provide interesting hypotheses, many studies have shown that enhancers and promoters can show substantial gains, losses, and reshuffling of TF binding sites, while maintaining a comparable regulatory activity (Ludwig et al. 2000; Dermitzakis and Clark 2002; Dermitzakis et al. 2003). A cisregulatory module (CRM) can show divergence not only by changing the composition of TF binding sites but also by gains and losses of entire CRMs around a gene locus (Wittkopp and Kalay 2012). "
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    ABSTRACT: Scoring the impact of non-coding variation on the function of cis-regulatory regions, on their chromatin state, and on the qualitative and quantitative expression levels of target genes is a fundamental problem in evolutionary genomics. A particular challenge is how to model the divergence of quantitative traits and to identify relationships between the changes across the different levels of the genome, the chromatin activity landscape, and the transcriptome. Here we examine the use of the Ornstein-Uhlenbeck (OU) model to infer selection at the level of predicted cis-regulatory modules, and link these with changes in transcription factor binding and chromatin activity. Using publicly available cross-species ChIP-seq and STARR-seq data we show how OU can be applied genome-wide to identify candidate transcription factors for which binding site and CRM turnover is correlated with changes in regulatory activity. Next, we profile open chromatin in the developing eye across three Drosophila species. We identify the recognition motifs of the chromatin remodelers, Trithorax-like and Grainyhead as mostly correlating with species-specific changes in open chromatin. In conclusion, we show in this study that CRM scores can be used as quantitative traits and that motif discovery approaches can be extended towards more complex models of divergence. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
    Molecular Biology and Evolution 05/2015; 32(9). DOI:10.1093/molbev/msv107 · 9.11 Impact Factor
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    • "For instance, orthologous enhancers might be interchangeable between different species without conspicuous DNA sequence similarity (Maduro and Pilgrim, 1996; Ludwig et al., 1998; Piano et al., 1999; Romano and Wray, 2003; Oda-Ishii et al., 2005). This is often attributed to the conservation of gene regulatory networks (GRNs) and the flexibility of TF binding site distribution in a given enhancer, which contribute to conservation of enhancer function (Ludwig et al., 2000; Oda-Ishii et al., 2005; Hare et al., 2008; Weirauch and Hughes, 2010). "
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    ABSTRACT: Ascidians present a striking dichotomy between conserved phenotypes and divergent genomes: embryonic cell lineages and gene expression patterns are conserved between distantly related species. Much research has focused on Ciona or Halocynthia spp. but development in other ascidians remains poorly characterized. In this study, we surveyed the multipotent myogenic B7.5 lineage in Molgula spp. Comparisons to the homologous lineage in Ciona revealed identical cell division and fate specification events that result in segregation of larval, cardiac, and pharyngeal muscle progenitors. Moreover, the expression patterns of key regulators are conserved, but cross-species transgenic assays uncovered incompatibility, or ‘unintelligibility’, of orthologous cis-regulatory sequences between Molgula and Ciona. These sequences drive identical expression patterns that are not recapitulated in cross-species assays. We show that this unintelligibility is likely due to changes in both cis- and trans-acting elements, hinting at widespread and frequent turnover of regulatory mechanisms underlying otherwise conserved aspects of ascidian embryogenesis. DOI:
    eLife Sciences 09/2014; 3:e03728. DOI:10.7554/eLife.03728 · 9.32 Impact Factor
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    • "At mutation-selection-drift equilibrium, a large number of genotypes will coexist (Figure 1), corresponding to different positions and numbers of phosphorylation sites in the PM domain. This stabilizing selection model has been applied to explain the rapid evolution of transcription factor binding sites in highly conserved developmental enhancers in drosophila (Ludwig et al., 2000). In one recent simulation study, clusters of transcription factor binding sites were shown to evolve spontaneously simply because there are a much larger number of genotypes with many binding sites that encode the trait than “simple” genotypes with few binding sites (He et al., 2012). "
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    ABSTRACT: Most proteins are regulated by posttranslational modifications and changes in these modifications contribute to evolutionary changes as well as to human diseases. Phosphorylation of serines, threonines, and tyrosines are the most common modifications identified to date in eukaryotic proteomes. While the mode of action and the function of most phosphorylation sites remain unknown, functional studies have shown that phosphorylation affects protein stability, localization and ability to interact. Two broad modes of action have been described for protein phosphorylation. The first mode corresponds to the canonical and qualitative view whereby single phosphorylation sites act as molecular switches that either turn on or off specific protein functions through direct or allosteric effects. The second mode is more akin to a rheostat than a switch. In this case, a group of phosphorylation sites in a given protein region contributes collectively to the modification of the protein, irrespective of the precise position of individual sites, through an aggregate property. Here we discuss these two types of regulation and examine how they affect the rate and patterns of protein phosphorylation evolution. We describe how the evolution of clusters of phosphorylation sites can be studied under the framework of complex traits evolution and stabilizing selection.
    Frontiers in Genetics 07/2014; 5:245. DOI:10.3389/fgene.2014.00245
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