Barrière Antoine, Ruvinsky Ilya
Department of Ecology and Evolution and Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America.
Department of Ecology and Evolution and Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America; Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, United States of America.
PLoS Genet. 2014 Jun 26;10(6):e1004435. doi: 10.1371/journal.pgen.1004435. eCollection 2014 Jun.
Because there is considerable variation in gene expression even between closely related species, it is clear that gene regulatory mechanisms evolve relatively rapidly. Because primary sequence conservation is an unreliable proxy for functional conservation of cis-regulatory elements, their assessment must be carried out in vivo. We conducted a survey of cis-regulatory conservation between C. elegans and closely related species C. briggsae, C. remanei, C. brenneri, and C. japonica. We tested enhancers of eight genes from these species by introducing them into C. elegans and analyzing the expression patterns they drove. Our results support several notable conclusions. Most exogenous cis elements direct expression in the same cells as their C. elegans orthologs, confirming gross conservation of regulatory mechanisms. However, the majority of exogenous elements, when placed in C. elegans, also directed expression in cells outside endogenous patterns, suggesting functional divergence. Recurrent ectopic expression of different promoters in the same C. elegans cells may reflect biases in the directions in which expression patterns can evolve due to shared regulatory logic of coexpressed genes. The fact that, despite differences between individual genes, several patterns repeatedly emerged from our survey, encourages us to think that general rules governing regulatory evolution may exist and be discoverable.
由于即使在亲缘关系密切的物种之间基因表达也存在相当大的差异，显然基因调控机制进化得相对较快。由于初级序列保守性并不能可靠地代表顺式调控元件的功能保守性，因此必须在体内对其进行评估。我们对秀丽隐杆线虫与亲缘关系密切的物种——布氏隐杆线虫、雷氏隐杆线虫、布伦纳隐杆线虫和日本隐杆线虫之间的顺式调控保守性进行了一项调查。我们通过将这些物种的八个基因的增强子导入秀丽隐杆线虫并分析它们驱动的表达模式，对其进行了测试。我们的结果支持了几个值得注意的结论。大多数外源顺式元件在与其秀丽隐杆线虫直系同源物相同的细胞中指导表达，证实了调控机制的总体保守性。然而，大多数外源元件在导入秀丽隐杆线虫后，也在内源模式之外的细胞中指导表达，这表明存在功能差异。不同启动子在同一秀丽隐杆线虫细胞中的反复异位表达可能反映了由于共表达基因的共享调控逻辑，表达模式在进化方向上的偏差。尽管各个基因之间存在差异，但我们的调查中反复出现了几种模式，这一事实促使我们认为可能存在并可发现调控进化的一般规则。
