Evolution of Drosophila melanogaster cis-regulatory modules

描述(由申请人提供)：当我们接近人类基因组测序将成为常规和广泛使用的时候，我们仍然令人惊讶地对序列变异的功能后果一无所知。尽管不完美，但利用我们对蛋白质结构、功能和进化的广泛知识的方法可以识别蛋白质编码基因中最有可能影响其功能的那些多态。然而，我们对非编码DNA中DNA序列与功能之间的关系缺乏了解，这使得我们基本上无法预测哪些多态性会产生生化、细胞或生物后果。我的研究重点是了解控制基因表达的非编码序列中序列变异和功能之间的关系。我用黑腹果蝇及其近亲的早期前后部模式作为模型。果蝇早期胚胎的基因调控是进行此类研究的一个极好的模型，因为对该系统的遗传和生化解剖有很长的历史，并且在过去的几年里它一直是广泛的实验基因组研究的目标。在目标1中，我提议使用目前可用的37个遗传上不同的黑腹果蝇品系的基因组来研究涉及基因调控的序列的选择模式。对基因组数据进行的完整的群体遗传学分析表明，作用于调控前后模式的转录因子结合位点的选择性作用力与基因组的其他部分没有显着差异。在目标2中，我将扩展这些研究，以包括所有这些全序列系胚胎中转录因子结合的实验调查数据(这些数据目前正在我的论文实验室生成)。我的目标是将观察到的转录因子结合的变异(或缺乏变异)与转录因子结合位点上的选择措施联系起来，并随后开发能够预测结合位点变异后果的模型。虽然这些研究将在模式生物中进行，但在果蝇和人类之间基因调控的基本机制上有广泛的保守性，我预计在果蝇中学到的经验将立即用于识别和理解与疾病和其他临床相关表型相关的人类非编码序列变异。 公共卫生相关性：随着人类基因组测序将成为常规和广泛使用的时代的到来，我们仍然令人惊讶地对序列变异的功能后果一无所知，特别是在绝大多数多态存在的非编码DNA中。果蝇早期前后部模式的模型提供了数以千计的功能非编码序列，在这些序列中我们可以分析自然发生的序列变异的影响。在果蝇身上学到的经验将立即用于识别和理解与疾病和其他临床相关表型相关的人类非编码序列变体。

DESCRIPTION (provided by applicant): As we approach a time when human genome sequencing will be routine and widely available, we remain surprisingly ignorant about the functional consequences of sequence variation. Although imperfect, methods that draw on our extensive knowledge of protein structure, function and evolution can identify those polymorphisms in protein-coding genes that are most likely to affect their function. However, our poor understanding of the relationship between DNA sequence and function in non-coding DNA, where the overwhelming majority of polymorphisms are found, makes it essentially impossible to predict which polymorphisms will have biochemical, cellular or organismal consequences. My research is focused on understanding the relationship between sequence variation and function in the non- coding sequences that control gene expression. I use as a model early anterior-posterior patterning in Drosophila melanogaster and its relatives. Gene regulation in the early Drosophila embryo is a superb model for such studies, as there is a long history of genetic and biochemical dissection of the system, and it has been the target of extensive experimental genomic studies in the past few years. In Aim 1, I proposed to use 37 currently available genomes of genetically distinct D. melanogaster lines to study patterns of selection on sequences involved in gene regulation. Completed population genetic analyses with genomic data suggest that the selective forces that have acted on the transcription factor binding sites that regulate anterior-posterior patterning are not significantly different than the rest of the genome. In Aim 2, I will extend these studies to include data from experimental surveys of transcription factor binding in embryos from all of these fully sequenced lines (these data are currently being generated in my thesis lab). My goal is to relate observed variation (or lack of variation) in transcription factor binding with measures of selection on transcription factor binding sites, and to subsequently develop models that can predict the consequences of variation in binding sites. Although these studies will be carried out in a model organism, there is extensive conservation in the basic mechanisms of gene regulation between flies and humans, and I expect that the lessons learned in Drosophila will be of immediate use in both identifying and understanding human non-coding sequence variants linked to disease and other clinically relevant phenotypes. PUBLIC HEALTH RELEVANCE: As we approach a time when human genome sequencing will be routine and widely available, we remain surprisingly ignorant about the functional consequences of sequence variation, particularly in non-coding DNA where the overwhelming majority of polymorphisms are found. The model of early anterior-posterior patterning in Drosophila melanogaster provides thousands of functional non-coding sequences in which we can assay the impact of naturally occurring sequence variations. The lessons learned in Drosophila will be of immediate use in both identifying and understanding human non-coding sequence variants linked to disease and other clinically relevant phenotypes.