Yeast as a model for understanding gene expression adaptation

项目摘要 通过自然选择的适应是一个过程，通过这个过程， 它的环境也发生了变化尽管它很重要，但我们仍然对它知之甚少。 遗传变异在任何物种中都是适应性的，以及这些变异在分子水平上是如何起作用的。 一个经典的问题是，大多数适应性变化是否涉及蛋白质序列的变化，或顺式- 监管要素21 -23;另一个基本问题是适应是否通常涉及单一的 大作用的突变，或小作用的许多突变23 -24。 从历史上看，大多数针对多态性状遗传基础的研究都集中在 蛋白质序列的变化影响很大，因为这些变化最容易识别。然而 最近的研究表明，多基因顺式调节适应实际上可能更为常见。 不幸的是，这些传统上几乎是不可能识别的，由于非常小的 每个变量对所选性状的个体影响。在过去的五年里，我们开发了一个 一种从全基因组数据中发现这些多基因适应的方法，基于“符号”的想法 测试“3，32。我们的目标是确定选择导致多个基因表达上调或下调的情况。 基因通过独立突变。在酵母中使用这种测试，我们已经确定了基因表达 包括毒素抗性33、麦角固醇生物合成13，40和致病性15的适应。总体而言，我们 符号测试的应用已经确定了数百个参与顺式调节的基因， 适应，包括基因表达适应的第一个例子发生在水平， 途径13和蛋白质复合物15;第一个已知的情况下，调节适应影响 行为14和致病性15;和多基因基因表达适应的任何第一个例子， 在家鼠和人类中也是如此。 在这个项目中，我们有两个主要目标。首先，我们将开发计算和实验 基于CRISPR/Cas9技术的工具，将使顺式调控变体的表征更加复杂。 在很多物种中都很实用。其次，我们将开发高通量映射的方法， 基因导致适应性的差异，这是自然选择的关键表型。该项目将 也为将来研究基因表达进化的各个方面奠定了基础， 人类健康，如基因表达如何在人类及其病原体中演变。

Project Summary Adaptation via natural selection is the process by which the incredible fit between every species and its environment has evolved. Despite its importance, we still have little understanding of which genetic variants have been adaptive in any species, and how these variants act at the molecular level. One classic question is whether most adaptations involve changes in protein sequences, or in cis- regulatory elements21-23; another fundamental question is whether adaptations typically involve single mutations of large effect, or many mutations of small effect23-24. Historically, most studies pinpointing the genetic basis of polymorphic traits have focused on protein sequence changes of large effect, because these have been the simplest to identify. However recent work has suggested that polygenic cis-regulatory adaptations may actually be far more common. Unfortunately these have traditionally been almost impossible to identify, due to the very small individual effect of each variant on the selected trait. Over the past five years, we have developed a method to find these polygenic adaptations from genome-wide data, based on the idea of a “sign test”3,32. The goal is to identify cases where selection has led to up- or down-regulation of multiple genes via independent mutations. Using this test in yeast, we have identified gene expression adaptations involving toxin resistance33, ergosterol biosynthesis13,40, and pathogenicity15. Overall, our applications of the sign test have identified several hundred genes involved in cis-regulatory adaptations, including the first examples of gene expression adaptation occurring at the level of pathways13 and protein complexes15; the first known cases of regulatory adaptations affecting behavior14 and pathogenicity15; and the first examples of polygenic gene expression adaptations of any kind in house mice14 and humans16. In this project we have two major goals. First, we will develop computational and experimental tools based on CRISPR/Cas9 technology that will make characterizing cis-regulatory variants far more practical in a wide range of species. Second, we will develop methods for high-throughput mapping of genes contributing to divergence in fitness, the key phenotype for natural selection. This project will also lay the groundwork for future investigations into facets of gene expression evolution important to human health, such as how gene expression evolves in both humans and their pathogens.