Constraints and Consequences of Copy Number Variation

拷贝数变异的限制和后果

• 批准号: 10385824
• 负责人: David Gresham
• 金额: $ 30.79万
• 依托单位: NEW YORK UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-01 至 2024-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10385824
• 关键词: Address; Alleles; Bar Codes; Biological Assay; Cells; Collection; Color; Complex; Copy Number Polymorphism; Costs and Benefits; Coupling; DNA; DNA Sequence; Data; Disease; Environment; Evolution; Fluorescence; Gene Dosage; Gene Duplication; Gene Expression; Gene Family; Gene Proteins; Generations; Genes; Genetic Variation; Genome; Genomic Segment; Genomics; Goals; Growth; Health; Heterogeneity; Human; Individual; Link; Maintenance; Methods; Modification; Molecular; Phenotype; Ploidies; Population; Process; Property; Proteins; Reporter; Resolution; Role; Saccharomyces cerevisiae; Saccharomycetales; Study models; System; Testing; Variant; Yeast Model System; Yeasts; cost; experience; fitness; genetic variant; genome sequencing; human disease; insight; microbial; molecular phenotype; novel; novel strategies; prevent; response; single-cell RNA sequencing; tumorigenesis; variant detection; whole genome

Project Summary/Abstract Copy number variants (CNVs) – increases and decreases in the number of copies of genomic regions – are a pervasive class of genetic variation that contribute to rapid adaptive evolution and human phenotypic variation and disease. Moreover, CNVs are the first step in processes that result in genome evolution such as gene family expansion and the generation of novel functions through modification of duplicate genes. Despite the importance of CNVs in human health and evolution, many fundamental questions about their role in evolving populations and their functional consequences remain unsolved. Experimental microbial evolution in chemostats is an ideal system for studying the evolutionary constraints and functional consequences of CNVs. To gain quantitative insights into the role of CNVs in evolving populations, we have developed a novel CNV reporter system using a constitutively expressed fluorescent protein gene linked to a locus at which CNVs are known to be repeatedly generated and selected. By coupling this system to a lineage tracking system using random molecular barcodes we have developed a powerful novel framework for studying the diversity and dynamics of CNVs in complex populations. We will use this novel system to address three fundamental questions. In aim 1, we will address the dynamics with which CNVs are selected in fluctuating environments. Using a combination of two-color CNV reporters and lineage tracking we will investigate the dynamics and diversity of CNV selection in variable chemostat environments. In aim 2, we will identify the determinants of CNV fitness effects. We will establish a collection of hundreds of unique CNV alleles that are molecularly characterized using whole genome sequencing and uniquely marked by DNA barcodes. We will use pooled fitness assays in a range of environmental conditions to quantify the fitness of each lineage and use these data to identify determinants of condition dependent and independent fitness fitness costs and benefits of CNVs. In aim 3, we will test the effect of CNVs on variability of gene expression and phenotypes. Using single cell RNA sequencing we will test whether CNVs results in increased variation in expression levels of both the genes contained within a CNV and all genes throughout the genome. We will also test whether CNVs result in increased variability in phenotypes using a high throughput microcolony growth rate assay. Our study will make use of the unparalleled efficiency and rigor afforded by the budding yeast model system and the unprecedented resolution provided by our new method for CNV detection to address fundamental questions of widespread significance for our understanding of CNVs in evolution and disease. As CNVs are universal in evolution and disease findings from our study will have a high impact on the field of genomics, evolution, and human health.

项目总结/摘要 拷贝数变异（CNVs）-基因组区域拷贝数的增加和减少-是一种基因突变。 一种普遍存在的遗传变异，有助于快速适应性进化和人类表型变异 和疾病此外，CNV是导致基因组进化的过程的第一步，例如基因突变。 家族扩展和通过修饰重复基因产生新功能。尽管 CNV在人类健康和进化中的重要性，许多关于它们在进化中的作用的基本问题， 人口及其功能后果仍然没有解决。实验微生物进化 恒化器是研究CNVs的进化约束和功能后果的理想系统。 为了定量了解CNV在进化人群中的作用，我们开发了一种新的CNV， 报告系统，其使用与CNV在其上表达的基因座连接的组成型表达的荧光蛋白基因。 已知被重复生成和选择。通过将该系统耦合到血统跟踪系统， 我们已经开发了一个强大的新框架，用于研究生物多样性， 复杂群体中CNVs的动态。我们将使用这个新系统来解决三个基本问题 问题.在目标1中，我们将讨论在波动环境中选择CNVs的动态。 使用双色CNV报告基因和谱系追踪的组合，我们将研究CNV的动态变化， 可变恒化器环境中CNV选择的多样性。在目标2中，我们将确定 CNV健身效果。我们将建立一个由数百个独特的CNV等位基因组成的集合， 使用全基因组测序进行表征，并通过DNA条形码进行唯一标记。我们将使用pooled 在一系列环境条件下的适应性测定，以量化每个谱系的适应性，并使用这些数据 确定条件依赖和独立的健身健身成本和效益的CNVs的决定因素。在 目的3，我们将测试CNVs对基因表达和表型变异性的影响。使用单细胞RNA 测序我们将测试CNVs是否导致两种基因表达水平的变异增加 包含在CNV和整个基因组中的所有基因中。我们还将测试CNVs是否会导致 使用高通量微菌落生长速率测定增加表型的可变性。我们的研究将 利用芽殖酵母模型系统提供的无与伦比的效率和严谨性， 我们的新方法为CNV检测提供了前所未有的分辨率，以解决以下基本问题： 对于我们理解CNVs在进化和疾病中的作用具有广泛的意义。由于CNV在 我们研究的进化和疾病发现将对基因组学、进化和 人体健康