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: 7486262
• 负责人: Sergey V Nuzhdin
• 金额: $ 29.61万
• 依托单位: UNIVERSITY OF SOUTHERN CALIFORNIA
• 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 2010-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7486262
• 关键词: Affect; Alleles; Architecture; Binding; Binding Sites; Biological Assay; Biology; Code; Collection; Complex; DNA; DNA Resequencing; Data; Data Set; Drosophila genome; Drosophila genus; Drosophila melanogaster; Frequencies; Functional RNA; Gene Expression; Gene Targeting; Genes; Genetic; Genetic Complementation Test; Genetic Polymorphism; Genetic Transcription; Genotype; Knock-out; Light; Measures; Medicine; Mind; Modeling; Natural Selections; Nature; Noise; Nucleic Acid Regulatory Sequences; Nucleotides; Pathway interactions; Performance; Phenotype; Population; Production; RNA; Relative (related person); Site; Standards of Weights and Measures; Testing; Tissues; Transcript; Transcriptional Regulation; Variant; design; fly; 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关键问题。最新的调控变异分析表明，大多数表型变异是由基因表达的改变引起的。转录起始、产生和稳定性受到影响转录水平的DNA多态性（表达多态性，EP）的影响，其中大约一半的改变是由于基因顺式调控区的EP。小作用的EP多还是大贡献的EP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，它们与转录因子中的反式多态性有多大的相互作用？它们是在保守的区域还是在物种之间快速进化的区域？在自然种群中分离的EP对生物体性能有什么影响？在某些生态环境或遗传背景中，它们是中性的、轻微有害的还是有益的？这些问题将通过重新测序调节和编码区（通常是基因）来回答-已知基因在转录水平上存在遗传差异，最好的研究是转录调节-在200个自然等基因系中。将使用来自整个身体或选择的组织的RNA与常见的标准等位基因进行比较，测量杂合果蝇中上述200种天然变化的等位基因的等位基因特异性表达.这将只提取顺式影响，同时大大减少环境影响，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。如果顺反相互作用普遍存在，则将采用染色体置换来使品系之间的遗传背景相等。为了确认候选EP的功能，将额外对1920个无关基因型进行基因分型和候选EP的表型分型。如此大的数据集将使得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。反式因子变化的影响及其相互作用也将被评估。对于转录因子结合的基因，提出了定量互补试验来研究转录因子多态性与EP之间的相互作用。这些研究将有助于建立一个复杂的字符变异的路径思想的描述。他们将阐明自然界中转录水平变异的遗传结构。