Genetic mechanisms and coevolutionary interactions in the evolution of gene expression divergence

基因表达差异进化中的遗传机制和共同进化相互作用

• 批准号: 10392889
• 负责人: Mohammad Siddiq
• 金额: $ 6.98万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10392889
• 关键词: Address; Affect; Alleles; Biological; Biological Assay; Biology; Case Study; Code; Data; Disease; Enhancers; Enzymes; Evolution; Gene Expression; Gene Expression Profiling; Gene Proteins; Genes; Genetic; Genetic Engineering; Genetic Epistasis; Genetic Processes; Genomics; Genotype; Glyceraldehyde-3-Phosphate Dehydrogenases; Growth; Individual; Investigation; Knowledge; Laboratories; Life; Measures; Metabolic; Metabolism; Methods; Molecular; Morphology; Mutagenesis; Mutation; Nucleotides; Penetrance; Phenotype; Phylogenetic Analysis; Play; Population; Process; Property; Proteins; Research; Resolution; Resources; Role; Saccharomyces; Site; Source; System; Technology; Testing; Variant; Work; Yeasts; enzyme activity; gene expression variation; gene synthesis; genetic regulatory protein; human disease; insight; knowledge base; novel; novel strategies; paralogous gene; programs; promoter; protein function; reconstruction; tool; trait

Project Summary: Phenotypic diversity and adaptation can result from changes in protein function or changes in gene expression. The importance of the former has always been recognized, but a growing body of work over the last two decades has established the equal or greater importance of the latter as well. Variation in cis- regulatory sequences—such as promoters and enhancers—has often been found to underlie differences in gene expression and cause evolutionary divergence across a wide range of traits, from metabolism to morphology. Despite many case studies implicating cis-regulatory changes in phenotypic divergence, the specific mutations and mechanisms responsible for changes in cis-regulatory activity often remain unknown. In addition, experimental investigations of how cis-regulatory changes coevolve with their cognate proteins and cause either evolutionary divergence or maintain functional conservation remain sparse. This knowledge gap has largely been caused by a combination of technical limitations and the circumstantial division of most empirical evolutionary research into programs that focus on either the study of gene expression or protein function, though the value of a combined approach is well-recognized. These limitations can now be overcome in some systems because of advances in technology and the capacity to use integrative approaches that characterize variation in gene expression and protein function. Consequently, key questions such as how changes in cis-regulatory sequences change gene expression, and how the effects of such mutations are shaped by genetic interactions and coevolution with proteins are now amenable to direct experimental investigation. Here, I propose to address these questions by studying gene expression divergence of TDH3 in Saccharomyces yeast, an ideal system in which the Wittkopp Laboratory’s expertise in gene expression can be combined with my background in protein evolution to gain novel, more complete insight into the process of phenotypic divergence. Specifically, I will use variation in TDH3 promoter function between two closely related species to investigate 1) how cis-regulatory mutations cause gene expression divergence, 2) how mutations in protein coding sequences coevolved with these changes in the cis-regulatory sequence and with paralogous genes to impact metabolic function, and 3) how epistasis causes cis-regulatory mutations to have different effects in different genetic contexts, in turn affecting the role of coevolution and mutational contingency in gene expression divergence. The proposed research will provide a rare nucleotide-level case study of how mutations and their context-dependent interactions cause functional divergence of a cis-regulatory sequence and contribute mechanistic insight into how evolution of regulatory sequences and their cognate proteins affect phenotypic evolution. The results of this study will also advance our basic understanding of regulatory mutations and epistasis and in turn the critical role these factors can play in human diseases and the variable penetrance of diseases in genetically different populations.

项目概述：表型多样性和适应性可以由蛋白质功能的变化或 in gene基因expression表达.前者的重要性一直得到承认，但越来越多的工作超过了 过去20年也确立了后者同等或更大的重要性。顺式变异 调控序列，如启动子和增强子，经常被发现是基因差异的基础， 基因的表达，并导致从代谢到形态的广泛性状的进化分歧。 尽管许多病例研究暗示表型分化中的顺式调节变化， 并且负责顺式调节活性变化的机制通常仍然未知。此外，本发明还提供了一种方法， 实验研究顺式调节变化如何与其同源蛋白共同进化， 进化分歧或维持功能保守仍然很少。这种知识差距在很大程度上 这是由于技术限制和大多数经验主义者的间接分歧造成的。 然而，进化研究的重点是基因表达或蛋白质功能的研究， 综合办法的价值是公认的。这些限制现在可以在某些系统中克服 由于技术的进步和使用综合方法的能力， 基因表达和蛋白质功能。因此，关键问题，如顺式调节的变化 序列改变基因表达，以及这些突变的影响如何通过遗传相互作用形成 与蛋白质的共同进化现在可以直接进行实验研究。 在这里，我建议通过研究TDH 3基因表达差异来解决这些问题， 酵母菌，这是一个理想的系统，可以利用维特科普实验室在基因表达方面的专业知识 结合我在蛋白质进化的背景，以获得新的，更完整的洞察过程， 表型趋异具体地说，我将使用TDH 3启动子功能在两个密切相关的 物种调查1）顺式调控突变如何导致基因表达分歧，2）突变如何在基因表达差异中发挥作用。 蛋白质编码序列与顺式调节序列中的这些变化以及与旁系同源物共同进化。 影响代谢功能的基因，以及3）上位性如何导致顺式调节突变产生不同的影响 在不同的遗传背景下，反过来又影响了基因的协同进化和突变偶然性的作用， 表达分歧这项拟议中的研究将提供一个罕见的核苷酸水平的案例研究， 并且它们的上下文依赖性相互作用引起顺式调节序列的功能分歧， 有助于深入了解调控序列及其同源蛋白质的进化如何影响 表型进化这项研究的结果也将推进我们对调控突变的基本认识 和上位性，反过来，这些因素在人类疾病中发挥的关键作用， 不同基因人群的疾病。