Collaborative Research: Discrete and Topological Models for Template-Guided Genome Rearrangements

21世纪科学的突破之一是通过RNA模板实现精确的基因组编辑。了解模板引导的基因组重排的社会影响可能是巨大的，它既是一种自然现象，如果被错误引导，可能导致疾病，如果加以利用，可能会导致下一代基因组编辑工具的出现。该项目旨在从理论和实验中了解rna模板DNA重组机制如何塑造某些纤毛虫物种的遗传信息组装，纤毛虫是天然基因组编辑水平最高的生物体。通过使用高通量实验工具和基于结理论和离散数学的新颖数学概念，该项目将获得程序化基因组重组过程的时间和结构洞察力，包括体细胞发育过程中DNA- DNA和DNA- RNA接触的全基因组调查。该项目将影响数学、生物和化学领域的博士后、研究生和本科教育，预计将产生至少两名博士后、三名博士和几篇高级论文。由于纤毛虫在发育过程中经历了成千上万的程序化DNA重排，比任何其他已知的生物都要多，我们使用Oxytricha及其近亲作为易于处理的实验室模型来研究模板引导的基因组重排。这个项目增加了我们对模板引导的染色体DNA重排的理解，无论是在核发育过程中，还是在产生混乱基因组的进化步骤中。先前的研究表明，协调这种重排过程的一般机制是由母体RNA模板指导的，该模板可以通过空间图进行数学建模，而重排途径可以建模为有向无环图中的路径，其顶点是空间图。该项目通过中间分子的镜头来解决这个问题，以及重排过程中出现的更高水平的相互作用，它将从实验和理论上检查全局重排途径。具体目标包括：1。实验解剖事件的时间顺序和DNA- DNA和DNA- RNA相互作用在基因组重排过程中的形成。2. 利用基于图的中间产物变化描述，建立基因组重排的数学方法。3. 建立数学模型，以衡量不同物种之间潜在的争夺模式的差异，以及可能的重排途径的差异。4. 启动基于图论、结论和代数拓扑的数学技术，提供对基因组解码途径结构模式的理解。该奖项反映了美国国家科学基金会的法定使命，并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，被认为值得支持。

One of the breakthroughs of 21st century science is the precise genome editing that is enabled through RNA templates. The societal impact of understanding template-guided genome rearrangement is potentially enormous, both as a natural phenomenon that, when mis-guided, can lead to disease, and that if harnessed could lead to the next generation of tools for genome editing. This project seeks to learn from both theory and experiments how a mechanism for RNA-templated DNA recombination sculpts the assembly of genetic information in certain species of ciliates, the organisms with the greatest levels of natural genome editing. Through use of high-throughput experimental tools and novel mathematical concepts based on knot theory and discrete mathematics, the project will gain temporal and structural insight into the process of programmed genome reorganization, including genome-wide surveys of DNA-- DNA and DNA--RNA contacts during somatic development in ciliates. The proposed research will impact postdoctoral, graduate and undergraduate education in mathematics, biology, and chemistry, with at least two postdocs, three PhDs and several senior theses expected to result from this project. Because the ciliate Oxytricha undergoes hundreds of thousands of programmed DNA rearrangements during development, more than any other known organism, we use Oxytricha and its close relatives as a tractable lab model to study template-guided genome rearrangements. This project increases our understanding of template-guided chromosomal DNA rearrangements, both during the process of nuclear development and across the evolutionary steps that gave rise to scrambled genomes. Previous studies have shown that the general mechanism that orchestrates this rearrangement process is guided by maternal RNA templates that can be mathematically modeled by spatial graphs, while the rearrangement pathways can be modeled as paths in a directed acyclic graph whose vertices are the spatial graphs. The project approaches the problem through the lens of the intermediate molecules, as well as the higher level interactions that arise during rearrangement, and it will examine both experimentally and theoretically the global rearrangement pathways. Specific aims include: 1. Experimental dissection of the temporal order of events and the formation of DNA-- DNA and DNA--RNA interactions during genome rearrangement. 2. Build mathematical methods for genome rearrangements using graph based descriptions of the changes in the intermediates. 3. Develop mathematical models to measure differences in underlying scrambling patterns, as well as differences in possible rearrangement pathways between different species. 4. Initiate mathematical techniques based on graph theory, knot theory and algebraic topology that provide understanding of the structural patterns of the genome unscrambling pathways.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.