Nucleotide polymorphisms responsible for expression variation in Drosophila

描述(申请人提供)：DNA多态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，大多数表型变异是由基因表达的改变引起的。影响转录水平的DNA多态(表达多态，EPs)影响转录本的起始、产生和稳定性，大约一半的变化是由于基因顺式调控区的EPs引起的。小效果的EP多还是贡献大的EP少？它们主要是在已知的影响转录的模块中还是在模块间区域？EP效应是相加的还是上位性的，它们与转录因子中的反式多态相互作用有多大？它们是在保守区域还是在物种间快速进化的区域？在自然种群中分离的EPs对生物体的表现有什么影响？在某些生态环境或遗传背景下，它们是中性的、略微有害的，还是有益的？这些问题将通过对200个自然的黑腹果蝇等基因系中的调控和编码区进行重新测序来回答-已知转录水平的基因在遗传上不同，最好的研究是转录调控。以上200个自然变异的等位基因在杂合子果蝇中的等位基因特异性表达将通过使用来自全身或选定组织的RNA与常见的标准等位基因进行比较来测量。这将只提炼顺式影响，同时大大减少环境影响和消除反式因素的噪音。关联测试将被用来识别影响成绩单水平的EP。如果顺式-反式相互作用普遍存在，将使用染色体替换来使品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进行1920个无关的基因分型和表型鉴定。如此大的数据集将允许根据所有分离的多态和它们之间的交互来对表达进行建模。还将评估反式因子的变化及其相互作用的影响。对于与转录因子(TF)结合的基因具有可用的敲除，提出了定量互补试验来研究转录因子与转录因子基因的多态之间的相互作用。这些研究将有助于建立对复杂特征变异的路径思维描述。他们将阐明自然界中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.