Yeast as a model for understanding gene expression adaptation

项目摘要 通过自然选择进行适应是每个物种之间令人难以置信的契合的过程 它的环境也发生了变化。尽管它很重要，但我们仍然对其中的 遗传变异在任何物种中都是适应的，以及这些变异在分子水平上是如何发挥作用的。 一个经典的问题是，大多数适应是涉及蛋白质序列的变化，还是涉及顺式基因的变化？ 监管要素21-23；另一个基本问题是，适应是否通常涉及单一 突变效应大，或突变多，效应小23-24。 从历史上看，大多数关于多态特征的遗传基础的研究都集中在 蛋白质序列变化的影响很大，因为这些都是最容易识别的。然而， 最近的研究表明，多基因顺式调节适应实际上可能要普遍得多。 不幸的是，这些传统上几乎不可能识别，因为非常小的 每个变种对所选性状的单独影响。在过去的五年里，我们制定了一项 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”的思想 测试“3，32。其目标是找出选择导致对多个 基因通过独立的突变。利用这项在酵母中的测试，我们已经确定了基因的表达 适应涉及毒素抗性33、麦角甾醇生物合成13、40和致病性15。总的来说，我们的 SIGN测试的应用已经确定了数百个与顺式调控有关的基因 适应，包括基因表达适应的第一个例子发生在 途径13和蛋白质复合体15；已知的第一个调节适应影响 行为14和致病性15；以及第一批多基因基因表达适应 家里有老鼠，人类有16种。 在这个项目中，我们有两个主要目标。首先，我们将开展计算和实验 基于CRISPR/Cas9技术的工具，将使表征顺式监管变体的能力大大增强 在广泛的物种中实用。第二，我们将开发高通量地图绘制方法 导致适应度差异的基因，这是自然选择的关键表型。这个项目将 也为未来研究基因表达进化的重要方面奠定了基础 人类健康，如基因表达如何在人类及其病原体中进化。

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.