Natural selection in a population of Drosophila melanogaster explained by changes in gene expression caused by sequence variation in core promoter regions.
Natural selection in a population of Drosophila melanogaster explained by changes in gene expression caused by sequence variation in core promoter regions.
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DOI：
10.1186/s12862-016-0606-3
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发表时间：
2016-02-09
影响因子：
3.4
通讯作者：
Kawata M
中科院分区：
文献类型：
--
作者：
Sato MP;Makino T;Kawata M
理解影响自然种群中基因调控区变异的进化力量是进化生物学的一个重要挑战，因为对这些变异的自然选择可以促进适应性表型进化。最近，全基因组序列分析已经确定了受自然选择的调控区域。然而，这些研究不能确定检测区域的序列变异与基因表达水平变化之间的关系。我们分析了核心启动子区域的序列变异，这是在高等真核生物中基因调控的关键区域，在果蝇的自然种群，并确定了核心启动子序列变异与基因表达水平的差异进行自然选择。在核心启动子区域的序列变异可以改变转录因子结合位点，并解释表达水平的差异，三个核心启动子区域被检测到作为候选人与纯化选择或选择性扫描和7个候选人与平衡选择，排除这些区域和核心启动子区域之间的连锁的可能性。CHKov 1，赋予对西格玛病毒和相关杀虫剂的抗性，被鉴定为已经进行选择性扫描的核心启动子区域，尽管不能否认核心启动子区域中的变异的选择是由于核心启动子区域外的调控区域中的连锁单核苷酸多态性。CHKov 1核心启动子区的核苷酸变化导致两个基础转录因子结合位点的丢失和一个转录因子结合位点的获得，导致基因表达水平降低。在与平衡选择相关的9个核心启动子区域中，brat和CG 9044与神经肌肉接头发育相关，Nmda 1与学习、行为可塑性和记忆相关。神经和行为特征的多样性可能是通过平衡选择来维持的。我们的研究结果揭示了进化过程中发生的自然选择的核心启动子区域的序列变异所造成的基因表达水平的差异在一个自然群体。核心启动子区域的序列甚至在种群内也是多样的，这可能为自然选择提供了来源。本文的在线版本（doi：10.1186/s12862-016-0606-3）包含补充材料，可供授权用户使用。
Understanding the evolutionary forces that influence variation in gene regulatory regions in natural populations is an important challenge for evolutionary biology because natural selection for such variations could promote adaptive phenotypic evolution. Recently, whole-genome sequence analyses have identified regulatory regions subject to natural selection. However, these studies could not identify the relationship between sequence variation in the detected regions and change in gene expression levels. We analyzed sequence variations in core promoter regions, which are critical regions for gene regulation in higher eukaryotes, in a natural population of Drosophila melanogaster, and identified core promoter sequence variations associated with differences in gene expression levels subjected to natural selection. Among the core promoter regions whose sequence variation could change transcription factor binding sites and explain differences in expression levels, three core promoter regions were detected as candidates associated with purifying selection or selective sweep and seven as candidates associated with balancing selection, excluding the possibility of linkage between these regions and core promoter regions. CHKov1, which confers resistance to the sigma virus and related insecticides, was identified as core promoter regions that has been subject to selective sweep, although it could not be denied that selection for variation in core promoter regions was due to linked single nucleotide polymorphisms in the regulatory region outside core promoter regions. Nucleotide changes in core promoter regions of CHKov1 caused the loss of two basal transcription factor binding sites and acquisition of one transcription factor binding site, resulting in decreased gene expression levels. Of nine core promoter regions regions associated with balancing selection, brat, and CG9044 are associated with neuromuscular junction development, and Nmda1 are associated with learning, behavioral plasticity, and memory. Diversity of neural and behavioral traits may have been maintained by balancing selection. Our results revealed the evolutionary process occurring by natural selection for differences in gene expression levels caused by sequence variation in core promoter regions in a natural population. The sequences of core promoter regions were diverse even within the population, possibly providing a source for natural selection. The online version of this article (doi:10.1186/s12862-016-0606-3) contains supplementary material, which is available to authorized users.