Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.
Science. 2011 Aug 19;333(6045):1019-24. doi: 10.1126/science.1202702.
The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory regions are conserved nonexonic elements (CNEEs), which are evolutionarily conserved yet do not overlap any coding or noncoding mature transcript. We then inferred the branch on which each CNEE came under selective constraint. Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.
基因调控元件的获得、丧失和修饰可能是动物谱系中表型变化的主要原因。为了研究整个脊椎动物进化过程中调控元件的获得，我们鉴定了包括人类在内的五种脊椎动物的全基因组假定调控区。这些假定的调控区是保守的非编码元件（CNEE），它们在进化上是保守的，但不与任何编码或非编码成熟转录本重叠。然后，我们推断了每个 CNEE 受到选择约束的分支。我们的分析确定了基因调控元件进化过程中的三个扩展时期。早期脊椎动物进化的特征是转录因子和发育基因附近的调控获得，但这一趋势被细胞外信号基因附近的创新所取代，然后是翻译后蛋白修饰物附近的创新。
