Adaptive evolution of gene expression in Drosophila melanogaster

描述(申请人提供)：尽管基因调控和转录处理在驱动细胞特化、组织特异性表达和形态发育方面具有重要意义，但对这些机制在适应性进化中的相对作用知之甚少。尽管对全球基因表达的研究已经成为人类疾病和健康研究的核心，但现有的统计工具不足以区分表达的适应性变化和归因于中性遗传结构的变化。顺式和反式调节是两种能够在基因表达中产生适应性变化的机制；这些机制中的每一种在驱动适应性变化中的意义尚不清楚。此外，选择性剪接被认为是导致mRNA转录多样性的主要因素，先前的工作表明，这种转录多样性包括异构体丰度的适应性变化以及显著的随机噪声成分。由于统计上的不足和异构体丰度变化的微妙，这些变化传达适应功能的比例是未知的，也很难估计。为了解决这些问题，我建议对反复适应冷应激的果蝇差异表达进行详细的RNA-Seq检测。从非洲和欧洲收集的一对低海拔和高海拔(和纬度)种群之间可遗传的耐冷性表型差异已经被鉴定出来，而可用于黑腹夜蛾的一系列基因组工具使其成为获得差异基因、等位基因和异构体表达的高分辨率测量的理想生物。我将从冷适应和温暖适应的果蝇中产生多个发育组织的全球表达谱，识别差异表达的基因座和剪接异构体。我将开发一种新的统计方法，解释中性的种群结构以及基因表达的高方差，以确定表达的功能变化。此外，我将从冷适应和暖适应的果蝇杂交中量化F1果蝇的等位基因特异性表达，揭示在两种跨调节背景下等位基因特异性表达的变化。根据这些等位基因特异性的估计，我可以确定亲本果蝇表达的适应性变化是顺式还是反式调节变化的结果。此外，通过检查 在温暖(祖先)和寒冷(衍生)处理中温暖适应和寒冷适应的果蝇中的表达，我可以确定基因表达功能的适应性变化是否创造了适应新环境的新的表达模式，或者在新的条件下引导祖先的表达模式。这项拟议的工作可以为理解适应性进化如何操纵基因表达模式提供无与伦比的力量。结合全基因组序列数据，我可以结合转录组学和群体基因组学来识别与基因和异构体表达的适应性变化相关的基因座和调节突变。

DESCRIPTION (provided by applicant): In spite of the significance of gene regulation and transcript processing in driving cellular specialization, tissue- specific expression, and morphological development, little is known concerning the relative role of these mechanisms in adaptive evolution. Although studies of global gene expression have become central to the study of human disease and health, the statistical tools available are not adequate in differentiating between adaptive changes in expression and those attributed to neutral genetic structure. Cis- and trans-regulation are two mechanisms capable of producing adaptive shifts in gene expression; the significance of each of these mechanisms in driving adaptive change is unclear. In addition, alternative splicing has been cited as a major contributor to mRNA transcript diversity, and previous work has suggested that this transcriptional diversity consists of a mixture of adaptive shifts in isoform abundance as well as a significant stochastic noise component. Due to statistical inadequacies and the subtlety of shifts in isoform abundance, the proportion of these changes conveying adaptive function is unknown and difficult to estimate. To address these issues, I propose detailed RNA-Seq examination of differential expression in Drosophila melanogaster following repeated adaptation to cold stress. Heritable phenotypic differences in cold tolerance between pairs of low- and high-altitude (and latitude) populations collected from Africa and Europe have already been identified and the range of genomic tools available for D. melanogaster make it the ideal organism to obtain high resolution measures of differential gene, allele, and isoform expression. I will generate global expression profiles from multiple developmental tissues in cold-adapted and warm-adapted flies raised in both warm and cold treatments, identifying differentially expressed loci and splicing isoforms. I will develop a novel statistical approach that accounts for neutral population structure as well as the high variance in gene expression to identify functional changes in expression. In addition, I will quantify allele-specific expression in F1 flies from crosses between cold- and warm-adapted flies, revealing shifts in allele-specific expression in both trans- regulatory backgrounds. From these allele-specific estimates, I can determine whether the adaptive shifts in expression identified in parental flies are the result of cis- or trans-regulatory changes. Also, by examining expression in both warm- and cold-adapted flies in warm (ancestral) and cold (derived) treatments, I can identify whether adaptive changes in gene expression function create novel expression patterns adaptive in the new environment, or canalize the ancestral expression pattern in the novel conditions. The proposed work can provide unparalleled power in understanding how adaptive evolution manipulates patterns of gene expression. In conjunction with whole genome sequence data, I can combine transcriptomics and population genomics to identify loci and regulatory mutations associated with adaptive changes in gene and isoform expression.