Khoueiry Pierre, Girardot Charles, Ciglar Lucia, Peng Pei-Chen, Gustafson E Hilary, Sinha Saurabh, Furlong Eileen Em
European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
Carl R. Woese Institute of Genomic Biology, University of Illinois, Champaign, United States.
Elife. 2017 Aug 9;6:e28440. doi: 10.7554/eLife.28440.
Sequence variation within enhancers plays a major role in both evolution and disease, yet its functional impact on transcription factor (TF) occupancy and enhancer activity remains poorly understood. Here, we assayed the binding of five essential TFs over multiple stages of embryogenesis in two distant species (with 1.4 substitutions per neutral site), identifying thousands of orthologous enhancers with conserved or diverged combinatorial occupancy. We used these binding signatures to dissect two properties of developmental enhancers: (1) potential TF cooperativity, using signatures of co-associations and co-divergence in TF occupancy. This revealed conserved combinatorial binding despite sequence divergence, suggesting protein-protein interactions sustain conserved collective occupancy. (2) Enhancer in-vivo activity, revealing orthologous enhancers with conserved activity despite divergence in TF occupancy. Taken together, we identify enhancers with diverged motifs yet conserved occupancy and others with diverged occupancy yet conserved activity, emphasising the need to functionally measure the effect of divergence on enhancer activity.
增强子内的序列变异在进化和疾病中都起着重要作用，但其对转录因子（TF）占据和增强子活性的功能影响仍知之甚少。在这里，我们检测了两个远缘物种（每个中性位点有1.4个替换）胚胎发生多个阶段中五种必需转录因子的结合情况，鉴定出数千个具有保守或不同组合占据的直系同源增强子。我们利用这些结合特征剖析了发育增强子的两个特性：（1）潜在的转录因子协同作用，利用转录因子占据中的共关联和共差异特征。这揭示了尽管序列存在差异，但仍有保守的组合结合，表明蛋白质-蛋白质相互作用维持了保守的集体占据。（2）增强子体内活性，揭示了尽管转录因子占据存在差异，但仍具有保守活性的直系同源增强子。综上所述，我们鉴定出了基序不同但占据保守的增强子，以及占据不同但活性保守的其他增强子，强调了从功能上测量差异对增强子活性影响的必要性。
