High-throughput precision genome editing to characterize natural genetic variants

高通量精确基因组编辑来表征自然遗传变异

• 批准号: 9978846
• 负责人: Hunter B Fraser
• 金额: $ 45.17万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-01 至 2023-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9978846
• 关键词: Address; Affect; Alleles; Animal Model; Automobile Driving; Binding Sites; Biology; Characteristics; Data; Dependence; Disease; Environment; Evolution; Genes; Genetic; Genetic Epistasis; Genetic Transcription; Genotype; Goals; Hybrids; Learning; Measures; Modeling; Molecular; Mutation; Natural Selections; Nature; Nucleic Acid Regulatory Sequences; Open Reading Frames; Organism; Pattern; Penetrance; Phenotype; Play; Process; Proteins; Research; Resolution; Ribosomes; Saccharomyces cerevisiae; Shapes; Sum; System; Technology; Untranslated RNA; Variant; Yeasts; base; combinatorial; experimental study; fitness; gene environment interaction; genetic variant; genome editing; genome-wide; human disease; insight; precise genome editing; promoter; sex; transcription factor; transcriptome sequencing

Project summary A major goal of genetics and evolutionary biology is to understand how changes in genotype affect phenotype. Genetic variants affecting fitness are especially informative for investigating evolution, since natural selection acts exclusively on these variants. By identifying specific variants that influence fitness, we can begin to understand the molecular mechanisms driving the incredible adaptations of all organisms to their respective environments. We recently developed an approach that allows us to edit genomes with unprecedented efficiency (~100%) and throughput. In our initial screen, we measured the fitness effects of 16,000 natural genetic variants differing between two strains of Saccharomyces cerevisiae. In this pilot experiment, we measured the effects of each variant in isolation, in a single condition. We found that nearly all strong fitness effects were from promoter variants, rather than protein-coding regions, and these were especially enriched at transcription factor binding sites. Here we propose to utilize this powerful system to investigate two types of interactions of fundamental importance: gene-by-environment (GxE) in Aim 1, and gene-by-gene (GxG, or epistasis) in Aim 2. Understanding the context-dependence of fitness effects will reveal key insights into the evolutionary process that would be unapproachable without our high-throughput precision genome editing technology. !

项目概要 遗传学和进化生物学的一个主要目标是了解基因型的变化如何影响 表型。影响适应性的遗传变异对于研究进化尤其有用，因为自然 选择专门作用于这些变体。通过识别影响健康的特定变异，我们可以开始 了解驱动所有生物体对其各自的令人难以置信的适应的分子机制 环境。 我们最近开发了一种方法，使我们能够以前所未有的效率编辑基因组 (~100%) 和吞吐量。在我们的初始筛选中，我们测量了 16,000 种自然基因的健身效果 两种酿酒酵母菌株之间存在差异的变体。在这个试点实验中，我们测量了 在单一条件下，每个变体的影响是孤立的。我们发现几乎所有强烈的健身效果都是 来自启动子变体，而不是蛋白质编码区，并且这些区域在转录时特别丰富 因子结合位点。 在这里，我们建议利用这个强大的系统来研究两种类型的基本相互作用 重要性：目标 1 中的基因与环境 (GxE) 和目标 2 中的基因与基因（GxG 或上位性）。 了解适应度效应的背景依赖性将揭示对进化过程的重要见解 如果没有我们的高通量精准基因组编辑技术，这是无法实现的。 ！