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

项目摘要：表型多样性和适应性可由蛋白质功能的变化或变化引起 在基因表达上。前者的重要性一直得到承认，但越来越多的工作结束了 过去二十年也确立了后者同等或更大的重要性。顺位变异-- 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。 表达并导致从新陈代谢到形态等一系列性状的进化差异。 尽管许多案例研究表明，表型分化中存在顺式调节变化，但特定的突变 而导致顺式调节活动变化的机制往往仍不清楚。此外, 顺式调节变化如何与它们的同源蛋白协同进化并导致 进化分化或维持功能守恒的情况仍然稀少。这种知识差距在很大程度上 是由技术限制和大多数经验主义的间接分歧共同造成的 对专注于基因表达或蛋白质功能研究的项目进行进化研究 综合方法的价值是公认的。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，这些方法表征了 基因表达和蛋白质功能。因此，关键问题，如顺式监管如何变化 序列改变了基因的表达，以及这种突变的影响是如何通过基因相互作用来塑造的 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TDH3在中国的基因表达差异来解决这些问题 酵母菌，一个理想的系统，维特科普实验室在基因表达方面的专业知识可以在其中 结合我在蛋白质进化方面的背景，对蛋白质进化的过程有了新的、更完整的洞察 表型分化。具体地说，我将使用TDH3启动子功能的变异在两个密切相关的 物种研究1)顺式调控突变如何导致基因表达差异，2)突变如何在 蛋白质编码序列与顺式调节序列中的这些变化以及与类似序列共同进化 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具有不同的影响 在不同的遗传背景下，反过来影响基因的协同进化和突变偶然性的作用 表达分歧。这项拟议的研究将提供一个罕见的核苷酸水平的案例研究，研究突变是如何 和它们的上下文相关的相互作用导致顺式调节序列的功能分歧和 有助于对调控序列及其同源蛋白的进化如何影响的机制洞察 表型进化。这项研究的结果也将促进我们对调控突变的基本理解 和上位性，进而这些因素在人类疾病和变量外显性中发挥关键作用 在遗传不同的人群中的疾病。

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.