Genetic Interactions and Synthetic Population Biology

描述（由申请人提供）：基因相互作用和合成群体生物学细胞行为是由相互作用的基因和蛋白质的电路决定的。在近亲繁殖的种群中，这些回路的组成部分是多种多样的：单个生物体包含不同的等位基因组，导致表型性状的变化。由于等位基因之间可能存在复杂的相互作用或上位性，因此将基因型和表型变异联系起来是具有挑战性的。也就是说，存在于一个位点上的等位基因可以改变另一个位点上的等位基因的相对效应。这些相互作用可以而且确实对从病毒获得耐药性到自闭症和其他复杂疾病的表型产生重大影响。然而，人们对遗传元素之间上位性强度的数量分布以及上位性相互作用对进化的影响知之甚少，特别是在有性繁殖的种群中。这些问题具有挑战性，因为它们需要研究基因多样化的人群，而不是无性繁殖的人群；依赖于有一个可靠的基因型和表型图谱和一个数学框架来定量解释进化动力学。因此，拟议的工作将涉及理论、计算和实验工作的结合。实验平台将以酿酒葡萄球菌为基础，并使用合成生物学方法来创建定义的相互作用遗传回路，允许定量表征和操纵上位性的性质和强度，并能够直接实时测量种群动态。我们的合作研究计划紧密结合了理论和实验方法以及Elowitz和Shraiman实验室的跨学科专业知识。更具体地说：(1)我们将建立理论模型，描述上位相互作用和重组对种群中等位基因和基因型动态的综合影响。这些模型将用于分析关键的群体遗传现象，包括遗传变异的维持、连锁不平衡和远交衰退。(2)我们将构建一套合成的遗传电路，在每个组件的替代等位基因之间具有可编程的上位相互作用。该系统将基于酿酒酵母的锌指转录调控模块，并将允许使用高通量单细胞荧光显微镜实时监测遗传多样性群体中的基因型分布。(3)我们将利用这个综合系统来检验有关遗传变异、远交衰退和连锁不平衡的具体理论预测。在这些实验中，遗传多样化的酵母群体（具有设计的相互作用等位基因）将在受控的选择压力下经历生长周期，然后是交配和重组。我们将使用单细胞荧光测量来跟踪基因型分布的动态，为与模型预测的比较提供定量数据。总之，这些目标将为在简化的近交实验室种群中操纵上位性相互作用以及理解自然近交种群中上位性相互作用的后果提供基础。

DESCRIPTION (provided by applicant): Genetic Interactions and Synthetic Population Biology Cellular behavior is determined by circuits of interacting genes and proteins. In outbred populations, the components of these circuits are diverse: individual organisms contain different sets of alleles causing variation in phenotypic traits. Relating genotypic and phenotypic variation is challenging because of the possibility of complex interactions, or epistasis, between the alleles. That is, the allele present at one locus can change the relative effect of an allele at another locus. These interactions can, and do, have large effects on phenotypes ranging from acquisition of drug resistance by viruses to autism and other complex disorders. However, little is known about the quantitative distribution of strength of epistasis between genetic elements and what consequences epistatic interactions have for evolution, especially in sexually reproducing populations. These questions are challenging because they require working with genetically diverse, rather than clonal, populations; depend on having a reliable map of genotypes and phenotypes and a mathematical framework for quantitative interpretation of evolutionary dynamics. Proposed work therefore will involve a combination of theoretical, computational and experimental work. The experimental platform will be based on S. cerevisiae and use the synthetic biology approach to create defined interacting genetic circuits, allow quantitative characterization and manipulation of the nature and strength of epistasis, and enable direct real time measurements of population dynamics. Our collaborative research plan tightly integrates theoretical and experimental approaches and the interdisciplinary expertise of the Elowitz and Shraiman laboratories. More specifically: (1) We will develop theoretical models describing the combined effect of epistatic interactions and recombination on the dynamics of alleles and genotypes in populations. These models will be used to analyze key population genetic phenomena, including maintenance of genetic variation, linkage disequilibrium, and outbreeding depression. (2) We will construct a set of synthetic genetic circuits with programmable epistatic interactions between alternative alleles for each component. This system will be based on zinc finger transcriptional regulation modules in S. cerevisiae, and will allow real-time monitoring of the genotype distribution within a genetically diverse population using high-throughput single-cell fluorescence microscopy. (3) We shall use this synthetic system to test specific theoretical predictions concerning genetic variation, outbreeding depression and linkage disequilibrium. In these experiments, genetically diverse yeast populations (with designed interacting alleles) will be subjected to cycles of growth under controlled selection pressure followed by mating and recombination. We will use single cell fluorescence measurements to follow the dynamics of the genotype distribution, providing quantitative data for comparison with model predictions. Together, these aims will provide a foundation for both manipulating epistatic interactions in a simplified outbred laboratory population, and understanding the consequences of epistatic interactions in natural outbred populations. PUBLIC HEALTH RELEVANCE: Proposed work will bridge systems biology and population genetics. The results will provide quantitative insight into the effect of epistatic interactions on the genetic structure of outbred populations. These fundamental issues are critical for understanding the link between population genetics and the observed complex disease phenotypes, and are thus central to the development of genomic medicine.