Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA.
PLoS Genet. 2010 Jan 22;6(1):e1000829. doi: 10.1371/journal.pgen.1000829.
The clustering of transcription factor binding sites in developmental enhancers and the apparent preferential conservation of clustered sites have been widely interpreted as proof that spatially constrained physical interactions between transcription factors are required for regulatory function. However, we show here that selection on the composition of enhancers alone, and not their internal structure, leads to the accumulation of clustered sites with evolutionary dynamics that suggest they are preferentially conserved. We simulated the evolution of idealized enhancers from Drosophila melanogaster constrained to contain only a minimum number of binding sites for one or more factors. Under this constraint, mutations that destroy an existing binding site are tolerated only if a compensating site has emerged elsewhere in the enhancer. Overlapping sites, such as those frequently observed for the activator Bicoid and repressor Krüppel, had significantly longer evolutionary half-lives than isolated sites for the same factors. This leads to a substantially higher density of overlapping sites than expected by chance and the appearance that such sites are preferentially conserved. Because D. melanogaster (like many other species) has a bias for deletions over insertions, sites tended to become closer together over time, leading to an overall clustering of sites in the absence of any selection for clustered sites. Since this effect is strongest for the oldest sites, clustered sites also incorrectly appear to be preferentially conserved. Following speciation, sites tend to be closer together in all descendent species than in their common ancestors, violating the common assumption that shared features of species' genomes reflect their ancestral state. Finally, we show that selection on binding site composition alone recapitulates the observed number of overlapping and closely neighboring sites in real D. melanogaster enhancers. Thus, this study calls into question the common practice of inferring "cis-regulatory grammars" from the organization and evolutionary dynamics of developmental enhancers.
转录因子结合位点在发育增强子中的聚类，以及聚类位点明显的优先保守性，已被广泛解释为证明转录因子之间的空间约束物理相互作用对于调控功能是必需的。然而，我们在这里表明，仅仅是增强子组成的选择，而不是其内部结构的选择，导致了聚类位点的积累，其进化动态表明它们是优先保守的。我们模拟了从果蝇（Drosophila melanogaster）理想化的增强子的进化，这些增强子仅受到一个或多个因子的最小数量的结合位点的限制。在这种约束下，只有当增强子中的其他地方出现补偿性结合位点时，破坏现有结合位点的突变才会被容忍。重叠的结合位点，如激活因子 Bicoid 和抑制因子 Krüppel 经常观察到的那样，其进化半衰期比同一因子的孤立结合位点长得多。这导致了重叠结合位点的密度远远高于预期的随机水平，并且出现了这些结合位点优先保守的现象。由于果蝇（像许多其他物种一样）偏爱缺失而不是插入，因此随着时间的推移，结合位点往往会彼此更接近，导致在没有任何聚类结合位点选择的情况下，结合位点总体上会聚类。由于这种效应对于最古老的结合位点最强，因此聚类结合位点也似乎优先被保守。在物种形成后，所有后代物种中的结合位点往往比共同祖先中的结合位点更接近，这违反了一个共同的假设，即物种基因组的共同特征反映了它们的祖先状态。最后，我们表明，仅仅基于结合位点组成的选择就可以重现真实果蝇增强子中观察到的重叠和紧密相邻结合位点的数量。因此，这项研究对从发育增强子的组织和进化动态推断“顺式调控语法”的常见做法提出了质疑。
