CAREER: Using indel rate variation to understand evolutionary constraints on distances between functional elements in the genome

相邻的蛋白质结构域相互作用折叠成一个功能性的蛋白质结构。DNA中相邻的结合位点与多蛋白复合物相互作用以实现有效结合。然而，蛋白质结构域和结合位点簇在基因组中都被编码为一维阵列。这个项目测试了这样一种假设，即为了实现特定和正确的相互作用，这些功能单元之间存在最佳距离，并且它们在进化过程中保持不变。由于DNA （indel）的插入和缺失改变了这些功能单元之间的距离，基因组将受到indel突变影响距离的进化约束。为了验证这一假设，研究者将开发软件来系统地估计和比较功能元素和统计模型之间距离的变化，以测试观察到的事件的可能性。项目完成后，科学界将拥有确定保守距离的工具，并将能够预测在这些基因组区域发生的indel突变的影响和重要性。研究者将为6-12年级的女孩们举办研讨会，以开发模拟进化约束概念的软件游戏。她还将为本科生和研究生开设有关分子进化和计算序列分析的实践课程。该项目的目标是利用索引率的变化来推断基因组中功能元件之间距离的进化约束。在针对蛋白质内的环和连接体或调节元件结合位点之间的空间中的索引的选择方面，实验证据已经积累起来。但是，由于难以对这些序列进行比对，对这些序列的进化研究几乎没有。该项目通过应用可以跨站点建模可变indel率的方法或建模长度的方法来解决这些挑战，而不是依赖于对齐。利用这些方法，研究者将对迄今为止被忽视的基因组的很大一部分进行系统发育和定量估计。在目标1中，使用研究者开发的新软件，将估算蛋白质基序之间的环的可变位点特异性索引率，以识别具有强烈距离约束的结构基序。在目标2中，研究者将开发一种基于出生-死亡过程的新软件，在不依赖对齐的情况下估计indel率。使用该软件，她将验证串联同源结构域与非同源结构域之间的距离有更强约束的假设。在Objective 3中，研究者将使用上述软件来检验假设，即同型二聚体的结合位点之间的距离比异源二聚体的结合位点之间的距离有更强的约束。本研究将结构生物学和发育生物学领域的知识整合到系统基因组的背景下，并为社区提供工具来测试特定的功能元件之间距离的进化假设。该项目的结果将在https://github.com/HanLabUNLV.This上公布，该奖项反映了美国国家科学基金会的法定使命，并通过基金会的智力价值和更广泛的影响审查标准进行评估，认为值得支持。

Adjacent protein domains interact to fold into a functional protein structure. Adjacent binding sites in the DNA interact with the multiprotein complex for efficient binding. Yet, both protein domains and clusters of binding sites are encoded as one-dimensional arrays in the genome. This project tests the hypothesis that, in order for specific and correct interactions to occur, there are optimal distances between these functional units and that they are maintained across evolutionary time. Since insertions and deletions of DNA (indels) change the distance between these functional units, the genome will be under evolutionary constraint against indel mutations that affect the distance. To test this hypothesis, the investigator will develop software to systematically estimate and compare the changes in distance between functional elements and statistical models to test the likelihood of the events observed. Upon project completion, the scientific community will have tools that identify distances that are conserved, and will be able to predict the effect and importance of indel mutations occurring in these genomic regions. The investigator will hold workshops for girls in grades 6-12 to develop software games that model the concept of evolutionary constraint. She will also develop undergraduate and graduate classes with hands-on activities on molecular evolution and computational sequence analysis.The goal of this project is to utilize the variation in rates of indels to infer the evolutionary constraint on the distance between functional elements in the genome. Experimental evidence has been accumulating on selection against indels in the loops and linkers within proteins, or in the space between binding sites of regulatory elements. But, studies on the evolution of these sequences are almost nonexistent, due to the difficulty in aligning these sequences. This project addresses these challenges by applying methods that can model variable indel rates across sites or methods that model length instead of relying on alignments. Using these methods, the investigator will produce phylogenetic, and quantitative estimates of indel rates on a significant proportion of the genome that has been neglected so far. In Objective 1, using a new software the investigator has developed, variable site-specific indel rates will be estimated across loops between protein motifs to identify structural motifs with strong constraints on their distance. In Objective 2, the investigator will develop a new software based on birth-death processes to estimate indel rates without relying on alignments. Using this software, she will test the hypothesis that there is stronger constraint on the distance between tandem homologous domains, compared to non-homologous domains. In Objective 3, the investigator will use the software described above to test the hypothesis that there is stronger constraint on the distance between binding sites of homodimers, compared to the distance between binding sites of heterodimers. This study will integrate the knowledge gained in the fields of structural biology and developmental biology into a phylogenomic context, and provide tools for the community to test specific evolutionary hypotheses on distance between functional elements of interest. The results of the project will be presented at https://github.com/HanLabUNLV.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.