Nucleotide polymorphisms responsible for expression variation in Drosophila

导致果蝇表达变异的核苷酸多态性

基本信息

批准号：
7662485
负责人：
Sergey V Nuzhdin
金额：
$ 29.53万
依托单位：
UNIVERSITY OF SOUTHERN CALIFORNIA
依托单位国家：
美国
项目类别：
财政年份：
2006
资助国家：
美国
起止时间：
2006-08-01 至 2011-07-31
项目状态：
已结题

项目摘要

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.

描述（由申请人提供）：DNA多态性如何导致复杂表型的变化仍然是生物学和医学的关键问题。最近对调节性变异的测定法表明，大多数表型偏差是由基因表达改变引起的。转录本的产生，产生和稳定性受DNA多态性（表达多态性，EPS）影响转录水平的影响，由于基因的顺式调节区域的EPS，大约有一半的改变。是否有许多小或几乎没有大量的EPS？它们主要是在已知会影响转录或模块间区域的模块中吗？ EP效应是添加剂还是上位性的，它们与转录因子中的反式多态性相互作用？它们是在保守的地区还是物种之间迅速发展的地区？ EPS在天然种群中隔离的影响对有机性能有何影响？它们在某些生态环境或遗传背景中是中性的，有害的还是有益的？这些问题将通过重新陈述调节和编码区域来解决这些问题，通常在基因上（转录水平上有遗传上已知，并且对转录调节）进行了最大的研究 - 在200天的果蝇果蝇天然同源线中。与使用全体或选定组织的RNA相比，将测量上述200个自然变化等位基因的等位基因表达。这只会大大减少环境影响并消除转移因素的噪声，这将仅蒸馏出来。关联测试将用于识别影响转录水平的EP。如果顺式相互作用是广泛的，则将采用染色体取代，以使线之间的遗传背景等效。为了确认候选EPS的功能，将对候选EPS进行基因分型和表型的额外基因型。如此大的数据集将以所有分离多态性及其之间的相互作用来实现表达建模。转移因素的变化及其相互作用的影响也将得到评估。对于由转录因子（TF）结合的带有可用敲除的基因，提出了定量互补测试来研究TFS中EPS与多态性之间的相互作用。这些研究将有助于建立对复杂角色变化的途径描述。他们将阐明自然界转录水平变化的遗传结构。