Adaptive evolution of gene expression in Drosophila melanogaster

描述（由申请人提供）：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，但这些机制在适应性进化中的相对作用知之甚少。虽然对全球基因表达的研究已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。顺式调控和反式调控是两种能够产生基因表达适应性转变的机制；这些机制在推动适应性变化中的重要性尚不清楚。此外，选择性剪接已被认为是mRNA转录多样性的主要贡献者，先前的研究表明，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同形丰度变化的微妙性，这些变化传达适应功能的比例是未知的，难以估计。为了解决这些问题，我提出了详细的RNA-Seq检测黑腹果蝇在反复适应冷应激后的差异表达。从非洲和欧洲收集的低海拔和高海拔（和纬度）种群之间的耐寒性遗传表型差异已经被确定，并且黑腹巨腹龙可用的基因组工具范围使其成为获得差异基因，等位基因和同种异构体表达的高分辨率测量的理想生物。我将从在冷热处理下饲养的冷适应和热适应果蝇的多个发育组织中生成全球表达谱，识别差异表达位点和剪接同工型。我将开发一种新的统计方法，该方法考虑中性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，我将量化来自冷适应和暖适应果蝇杂交的F1果蝇的等位基因特异性表达，揭示等位基因特异性表达在两种反调控背景下的变化。根据这些等位基因特异性的估计，我可以确定亲本果蝇中表达的适应性变化是否是顺式或反式调节变化的结果。同时，通过检查

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.