Nucleotide polymorphisms responsible for expression variation in Drosophila

导致果蝇表达变异的核苷酸多态性

• 批准号: 7142883
• 负责人: Sergey V Nuzhdin
• 金额: $ 28.76万
• 依托单位: UNIVERSITY OF CALIFORNIA AT DAVIS
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-08-01 至 2007-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7142883
• 关键词: Drosophilidae; animal population genetics; arthropod genetics; genetic polymorphism; genetic regulation; genetic regulatory element; genetic transcription; genotype; nucleic acid sequence; phenotype; polymerase chain reaction; transcription factor

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异仍然是生物学和医学中的一个关键问题。最近的调控变异分析表明，大多数表型偏差是由基因表达的改变引起的。转录本的起始、产生和稳定性受到影响转录本水平的 DNA 多态性（表达多态性，EP）的影响，大约一半的改变是由基因顺式调控区域的 EP 引起的。小效应 EP 较多还是贡献较大的 EP 较少？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 效应是累加性的还是上位性的？它们与转录因子中反式多态性的相互作用有多大？它们是在保守区域还是在物种之间快速进化的区域？自然群体中 EP 的分离对机体性能有何影响？它们在某些生态环境或遗传背景中是中性的、稍微有害的还是有益的？这些问题将通过对黑腹果蝇 200 个天然同基因系中的调控和编码区域（已知转录水​​平在遗传上存在差异，并且对转录调控进行了深入研究）的基因调控和编码区域进行重新测序来回答。将使用来自全身或选定组织的RNA与常见标准等位基因进行比较，测量杂合果蝇中上述200个自然变化等位基因的等位基因特异性表达。这将仅提取顺式影响，同时大大减少环境影响并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 EP。如果顺式-反式相互作用广泛存在，则将采用染色体替换以使品系之间的遗传背景相等。为了确认候选EP的功能，将对候选EP另外对1920个不相关的基因型进行基因分型和表型分析。如此大的数据集将能够根据所有分离的多态性及其之间的相互作用对表达进行建模。还将评估反式因子变化的影响及其相互作用。对于具有可用敲除的转录因子（TF）结合的基因，提出了定量互补测试来研究 EP 和 TF 多态性之间的相互作用。这些研究将有助于建立复杂性格变异的路径思维描述。他们将揭示自然界转录水平变异的遗传结构。