Gene expression and adaptive noncoding changes during human evolution.
Gene expression and adaptive noncoding changes during human evolution.
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DOI：
10.1186/s12864-017-3831-2
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发表时间：
2017-06-05
期刊：
影响因子：
4.4
通讯作者：
Wray GA
中科院分区：
文献类型：
--
作者：
Babbitt CC;Haygood R;Nielsen WJ;Wray GA
尽管有证据表明，在人类进化过程中，基因表达和非蛋白质编码（假定的基因组调控区域）都发生了适应性变化，但基因表达与顺式调控区域适应性变化之间的关系仍不清楚。在这里，我们提出了人类和黑猩猩五种组织中基因表达的新测量方法，并用它们来评估这种关系。然后，我们将我们的结果与先前的适应性非编码变化研究进行比较，在基因本体组的水平上分析相关性，以获得检测相关性的统计能力。与以往的研究一致，我们发现在个体基因水平上，基因表达与适应性非编码变化之间的相关性很小；然而，我们确实在生物功能本体组的水平上发现了显著的相关性。功能的类型包括由特定转录因子调节的过程，对遗传或化学扰动的反应，以及免疫系统内细胞类型的分化。在差异表达和非编码适应共同富集的功能类别中，突出的主题包括癌症，特别是上皮性癌症，以及神经发育和功能。本文的在线版本（doi:10.1186/s12864-017-3831-2）包含补充材料，可供授权用户使用。
Despite evidence for adaptive changes in both gene expression and non-protein-coding, putatively regulatory regions of the genome during human evolution, the relationship between gene expression and adaptive changes in cis-regulatory regions remains unclear. Here we present new measurements of gene expression in five tissues of humans and chimpanzees, and use them to assess this relationship. We then compare our results with previous studies of adaptive noncoding changes, analyzing correlations at the level of gene ontology groups, in order to gain statistical power to detect correlations. Consistent with previous studies, we find little correlation between gene expression and adaptive noncoding changes at the level of individual genes; however, we do find significant correlations at the level of biological function ontology groups. The types of function include processes regulated by specific transcription factors, responses to genetic or chemical perturbations, and differentiation of cell types within the immune system. Among functional categories co-enriched with both differential expression and noncoding adaptation, prominent themes include cancer, particularly epithelial cancers, and neural development and function. The online version of this article (doi:10.1186/s12864-017-3831-2) contains supplementary material, which is available to authorized users.