Compensatory Evolution of Gene Expression
Compensatory Evolution of Gene Expression
复制标题
基因表达的补偿性进化
DOI：
10.1016/j.tig.2019.09.008
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发表时间：
2019
影响因子：
11.4
通讯作者：
Nuzhdin, Sergey V.
中科院分区：
文献类型：
--
作者：
Signor, Sarah A.;Nuzhdin, Sergey V.
顺式和反式组分对进化有许多重要的贡献，包括，例如，种间与种内变异或环境特异性表型进化中顺式和反式差异的频率[1]。人们经常观察到，成对的顺式-反式差异更经常是补偿性的（+/-），而不是放大性的（-/-;+/+）。最近已经确定了与从比较等位基因特异性表达与亲本菌株之间的表达差异的实验中推断补偿性顺式和反式调节进化相关的混杂因素[2-4]，这对先前研究报告的调节进化中补偿性变化的作用提出了质疑。然而，正如我们后面所描述的，补偿性变化在调节进化中是常见的证据并不仅仅来自这种类型的实验，考虑到等位基因特异性表达分析的这种局限性后，剩余的证据仍然表明，补偿性变化在调节进化中是常见的。表达数量性状基因座（eQTL）分析将分子表型（如基因表达）与遗传变异相关联，并且通常发现拮抗性顺式和反式效应的富集，其总体上用于使基因表达水平正常化（尽管eQTL通常具有检测trans-eQTL的低能力）[5]。基因缺失实验发现，基因组中其他地方的突变可以补偿缺失的影响[6]。另一种方法确定了顺式差异和整体基因表达差异，但没有明确检测到反式差异。这项工作发现，虽然顺式调节分歧随着时间的推移而增加，
cis and trans components has contributed many important insights into evolution, including, for example, the frequency of cis and trans differences in interspecific versus intraspecific variation or the evolution of environmentspecific phenotypes[1]. It has frequently been observed that cis–trans differences found in pairs are more frequently compensatory (+/–) rather than amplifying (–/–;+/+). A confounding factor associated with inferring compensatory cis-and trans-regulatory evolution from experiments comparing allele-specific expression to expression differences between parental strains has recently been identified [2–4], calling into question the role of compensatory changes in regulatory evolution reported by prior studies. However, as we describe later, evidence for compensatory changes being common in regulatory evolution does not come solely from this type of experiment, and the body of evidence remaining after taking this limitation of the allele-specific expression analysis into account still suggests that compensatory changes are common in regulatory evolution.Evidence for compensatory evolution comes from a variety of study designs. Expression quantitative trait loci (eQTL) analysis correlates a molecular phenotype, such as gene expression, with genetic variation, and often finds an enrichment of antagonistic cis and trans effects which overall serve to normalize levels of gene expression (though eQTLs often have low power to detect trans-eQTL)[5]. Gene deletion experiments have found that the effects of a deletion are compensated for by mutations elsewhere in the genome [6]. Another approach identified cis differences and overall gene expression divergence but did not explicitly detect trans differences. This work found that while cis-regulatory divergence increased over time be-