Cis-regulatory motif variants and evolution of gene regulation in yeasts

酵母中顺式调控基序变异和基因调控进化

• 批准号: 7301592
• 负责人: WEN-HSIUNG LI
• 金额: $ 20.73万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-01 至 2010-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7301592
• 关键词: Accounting; Affinity; Alleles; Alzheimer' s Disease; Asses; Binding; Binding Sites; Candida albicans; Code; Complex; Data; Disease; Etiology; Evolution; Gene Expression; Gene Expression Regulation; Gene Targeting; Genes; Genome; Goals; HIV; Heart Diseases; Hybrids; Methods; Modeling; Molecular Profiling; Mutation; Noise; Nucleotides; Numbers; Pathology; Pattern; Physiology; Positioning Attribute; Range; Research; Risk; Saccharomyces; Saccharomyces cerevisiae; Site; Site-Directed Mutagenesis; Testing; Thinking; Transcription factor genes; Validation; Variant; Work; Yeasts; alpha-Thalassemia; cofactor; promoter; transcription factor; transmission process

DESCRIPTION (provided by applicant): Variants of a transcription factor (TF) binding motif among genes are commonly thought to be functionally equivalent (degenerate), but some of them may in fact influence gene expression; such a variant is called a "functional" variant. Little is known about how or when these functional variants act, and how to detect them. Our goal is to understand the extent that TF binding site variants contribute to expression variation among genes in a genome or between genes in different species. Our aims are to: A. Characterize functional TF binding site variants in yeast using computational approaches, (a) Develop robust methods to account for multiple binding sites of the TF, degeneracy within functional variants, expression noise, and non-independence of all-by-all comparisons of genes and binding site variants, (b) Elucidate the patterns of conservation of variant-specific expression profiles, looking across Saccharomyces sensu stricto species and between these species and C. albicans to determine whether the function of target genes of TFs or the sequence composition of the motif is associated with the conservation of functional variants, (c) Characterize nucleotide substitutions in target gene promoters that may have caused a switch in variant-specific expression profiles between species B. Experimentally validate and characterize functional variants, (a) Alter nucleotides at variant binding site positions using site-directed mutagenesis to test for predicted expression changes. A number of variant sites in S. cerevisiae will be selected for experimental validation. Further, the effect of variant switches between S. cerevisiae and S. paradoxus will be validated by allele-specific expression analysis in a hybrid strain, (b) Test models for the mechanism of variant binding site function. The proposed research will increase our understanding of the complex cis-regulatory code that underlies physiology and pathology. As mutations in promoters have been associated with heart disease, HIV transmission risk, alpha-thalassemia, Alzheimer's and other diseases, understanding the full range of function of a binding site could be critical for assessing mutations that are associated with disease etiology.

描述（由申请人提供）：基因之间转录因子（TF）结合基序的变体通常被认为是功能等效的（退化），但其中一些实际上可能影响基因表达；这样的变体称为“功能”变体。这些功能变体如何或何时何时了解它们，以及如何检测它们，知之甚少。我们的目标是了解TF结合位点变异有助于基因组中基因之间或不同物种中基因之间的表达变异。我们的目的是：A。使用计算方法来表征酵母中功能性TF结合位点变体，（a）开发出可靠的方法来说明TF的多个结合位点，功能变体中的脱位性，表达噪声，无独立的全部依赖性基因和结合位点变异的全部比较，（b）阐明了变异特异性表达谱的保守模式，跨糖疗法sensu sensu sensu stricto物种以及这些物种和白色念珠菌之间的含量是否确定TFS的靶基因的功能或基序的序列组成与功能变体的保守性有关，（c）表征靶基因启动子中核苷酸取代，这可能导致物种B之间变异特异性表达谱的转换。实验验证和表征功能变体（（ a）使用位置定向诱变来测试预测的表达变化，在变异结合位置的位置上改变核苷酸。将选择酿酒酵母中的许多变体位点进行实验验证。此外，酿酒酵母和悖论链球菌之间的变体开关的影响将通过混合菌株中的等位基因特异性表达分析来验证（b）（b）测试模型，用于变异结合位点功能的机理。拟议的研究将提高我们对生理和病理基础的复杂顺式调节法规的理解。由于启动子中的突变与心脏病，HIV传播风险，α-丘脑贫血，阿尔茨海默氏症和其他疾病有关，因此了解结合位点的全部功能对于评估与疾病病因相关的突变至关重要。