Nucleotide polymorphisms responsible for expression variation in Drosophila

描述（由申请人提供）：DNA多态性如何导致复杂表型的变异仍然是生物学和医学中的一个关键问题。最近对调节变异的分析表明，大多数表型偏差是由基因表达的改变引起的。转录物的起始、产生和稳定性受到影响转录物水平的DNA多态性（表达多态性，EPs）的影响，大约一半的改变是由基因顺式调控区域的EPs引起的。影响小的每股收益多还是贡献大的每股收益少？它们主要是在已知影响转录的模块中还是在模块间区域中？EP效应是加性的还是上位性的？它们在多大程度上与转录因子的反式多态性相互作用？它们是在受保护的地区还是在物种之间快速进化的地区？自然种群中EPs的分离对机体性能有何影响？在某些生态环境或遗传背景下，它们是中性的、轻微有害的还是有益的？这些问题将通过对200个天然黑腹果蝇等基因系的基因调控区和编码区进行重测序得到解答。这些基因在基因转录水平上是不同的，并且在转录调控方面得到了最好的研究。以上200个自然变化的等位基因在杂合果蝇中的特异表达将使用来自整个身体或选定组织的RNA与普通标准等位基因进行比较。这将提炼顺式影响，同时大大减少环境影响和消除反式因素的噪音。关联测试将用于识别影响转录水平的EPs。如果顺式-反式相互作用广泛存在，染色体替换将使各系之间的遗传背景相等。为了确认候选EPs的功能，将对候选EPs的1920个不相关基因型进行额外的基因分型和表型分析。如此庞大的数据集将能够根据所有分离的多态性和它们之间的相互作用对表达进行建模。反式因子变异的影响及其相互作用也将被评估。对于具有敲除基因的转录因子（TF）结合的基因，提出了定量互补测试来研究EPs与TF多态性之间的相互作用。这些研究将有助于建立一种基于路径的复杂性状变异描述。它们将揭示自然界转录水平变异的遗传结构。

DESCRIPTION (provided by applicant): How DNA polymorphisms result in variation in complex phenotypes remains a key question in biology and medicine. Recent assays of regulatory variation suggest that the majority of phenotypic deviations are caused by alterations in gene expression. Transcript initiation, production, and stability are affected by DNA polymorphisms (expression polymorphisms, EPs) affecting transcript level, with approximately a half of all alterations due to EPs in cis-regulatory regions of genes. Are there many small-effect or few large- contribution EPs? Are they mostly in modules known to affect transcription or in intermodule regions? Are EP effects additive or epistatic, and how much do they interact with trans polymorphisms in transcription factors? Are they in conserved regions or those evolving quickly between species? What are the effects of EPs segregating in natural populations on organismal performance? Are they neutral, slightly deleterious, or beneficial in some ecological settings or genetic backgrounds? These questions will be answered by resequencing regulatory and coding regions often genes - known to genetically vary for transcript level, and best studied for transcription regulation - in 200 natural isogenic lines of Drosophila melanogaster. Allele- specific expression of the above 200 naturally varying alleles in heterozygous flies will be measured in comparison to common standard alleles using RNA from whole bodies or selected tissues. This will distill cis- influences only while greatly reducing environmental effects and eliminating noise from trans- factors. Association tests will be used to identify EPs affecting transcript level. If cis- by trans- interactions are widespread, chromosomal substitutions will be employed to make the genetic background equivalent among lines. To confirm the function of candidate EPs, 1920 unrelated genotypes will be additionally genotyped and phenotyped for candidate EPs. Such a large data set will enable modeling of expression in terms of all the segregating polymorphisms and interactions between them. Effects of variations in trans- factors, and their interactions will also be evaluated. For the genes bound by transcription factors (TF) with available knockouts, quantitative complementation tests are proposed to study interactions between EPs and polymorphisms in TFs. These studies will contribute to building a pathway-minded description of complex character variation. They will shed light on the genetic architecture of transcript level variation in nature.