Natural selection on cis and trans regulation in yeasts
Natural selection on cis and trans regulation in yeasts
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DOI：
10.1101/gr.101576.109
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发表时间：
2010-06-01
期刊：
影响因子：
7
通讯作者：
Li, Wen-Hsiung
中科院分区：
文献类型：
--
作者：
Emerson, J. J.;Hsieh, Li-Ching;Li, Wen-Hsiung
基因表达受顺式元件和反式因子的调节，顺式元件是与它们调节的基因紧密相连的DNA片段，反式因子通常是能够扩散到未连接基因的蛋白质。了解调控变异的模式和来源对于理解表型和基因组进化至关重要。在这里，我们通过深度测序测量全基因组等位基因特异性表达，以研究两种酿酒酵母菌株之间的顺式和反式表达变异模式。我们提出了一个统计建模框架的基础上的二项分布，同时解决标准化的读取计数来自不同的父母和估计的顺式和反式表达变异参数。我们发现，在酵母表达多态性是常见的顺式和反式，虽然反式变异更常见。表达进化中的限制与其他限制的标志相关，包括基因的必要性，蛋白质相互作用伴侣的数量，以及氨基酸取代的限制，表明顺式和反式多态性都明显受到纯化选择的影响，尽管反式变异似乎对选择性限制更敏感。比较S.酿酒酵母和酿酒酵母。与我们的种内变异相矛盾，表明与分子进化的中性模型有重大偏离。进一步研究多态性和分歧之间的相关性表明，顺式分歧更频繁地介导的积极达尔文选择比反式分歧。
Gene expression is regulated both by cis elements, which are DNA segments closely linked to the genes they regulate, and by trans factors, which are usually proteins capable of diffusing to unlinked genes. Understanding the patterns and sources of regulatory variation is crucial for understanding phenotypic and genome evolution. Here, we measure genome-wide allele-specific expression by deep sequencing to investigate the patterns of cis and trans expression variation between two strains of Saccharomyces cerevisiae. We propose a statistical modeling framework based on the binomial distribution that simultaneously addresses normalization of read counts derived from different parents and estimating the cis and trans expression variation parameters. We find that expression polymorphism in yeast is common for both cis and trans, though trans variation is more common. Constraint in expression evolution is correlated with other hallmarks of constraint, including gene essentiality, number of protein interaction partners, and constraint in amino acid substitution, indicating that both cis and trans polymorphism are clearly under purifying selection, though trans variation appears to be more sensitive to selective constraint. Comparing interspecific expression divergence between S. cerevisiae and S. paradoxus to our intraspecific variation suggests a significant departure from a neutral model of molecular evolution. A further examination of correlation between polymorphism and divergence within each category suggests that cis divergence is more frequently mediated by positive Darwinian selection than is trans divergence.