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以折叠成功能性蛋白质结构。DNA中的相邻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都被编码为基因组中的一维阵列。这个项目测试的假设，为了发生特定的和正确的相互作用，有这些功能单位之间的最佳距离，他们在进化的时间保持。由于DNA的插入和缺失（indel）改变了这些功能单位之间的距离，因此基因组将受到影响距离的indel突变的进化约束。为了检验这一假设，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的距离变化，以检验观察到的事件的可能性。项目完成后，科学界将拥有识别保守距离的工具，并能够预测这些基因组区域中发生的indel突变的影响和重要性。研究人员将为6-12年级的女孩举办研讨会，开发模拟进化约束概念的软件游戏。她还将开发本科生和研究生课程，并在分子进化和计算序列分析方面进行实践活动。该项目的目标是利用indels速率的变化来推断基因组中功能元件之间距离的进化约束。针对蛋白质内的环和接头中或调节元件的结合位点之间的空间中的indel的选择的实验证据已经积累。但是，这些序列的进化研究几乎是不存在的，由于这些序列的比对困难。该项目通过应用可以模拟不同位点的可变插入缺失率的方法或模拟长度而不是依赖于比对的方法来解决这些挑战。使用这些方法，研究人员将产生系统发育，并在迄今为止被忽视的基因组的显着比例的indel率的定量估计。在目标1中，使用研究人员开发的新软件，将在蛋白质基序之间的环上估计可变的位点特异性插入缺失率，以识别对其距离有很强限制的结构基序。在目标2中，研究人员将开发一种基于出生-死亡过程的新软件，以估计indel率，而不依赖于比对。使用该软件，她将测试以下假设：与非同源结构域相比，串联同源结构域之间的距离受到更强的约束。在目标3中，研究者将使用上述软件来检验以下假设：与异源二聚体的结合位点之间的距离相比，同源二聚体的结合位点之间的距离存在更强的约束。这项研究将把结构生物学和发育生物学领域的知识整合到一个新的基因组背景下，并为社区提供工具，以测试特定的进化假说之间的距离感兴趣的功能元件。该项目的结果将在www.example.com上公布https://github.com/HanLabUNLV.This奖项反映了NSF的法定使命，并被认为值得通过使用基金会的知识价值和更广泛的影响审查标准进行评估来支持。

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.