DMS/NIGMS 2: Collaborative Research: Modeling R-Loop Formation and Topology Using Braids and Graphs Coupled with Single-Molecule Footprinting

生命的两个姐妹分子RNA和DNA的相互作用长期以来一直是科学研究的焦点。最近发现了一种新的分子复合物，称为R环，由DNA双链体和RNA链组成。已经发现，R环是普遍存在的，并且被证明是在从细菌到哺乳动物的整个生命王国中观察到的功能上重要的结构。 R环现在被认为是一种新型的信号，在越来越多的生物过程中发挥重要作用。R环形成缺陷与包括人类在内的多种物种的疾病有关。然而，目前对R环的形成和结构了解甚少。该项目将解决控制R环起始的力，R环开始和终止的方式，RNA-DNA复合物的几何形状，以及决定R环稳定性的因素。这项工作将推进数学和生物学领域，同时通过将理论方法与实验工作相结合来加强它们之间的相互联系。该研究为实验和数学生物学的博士后，研究生和本科生培训提供了新的途径，并包括专门由女性数学家提供的指导部分，以支持他们的科学参与并提高他们的知名度。研究结果将广泛传播。R环是由RNA：DNA双链体和DNA单链组成的三链结构。最初在细菌中发现，R环可以占酵母，植物和哺乳动物基因组的3-5%。本计画利用新颖的数学方法来研究DNA序列与DNA拓扑结构对R-环形成的影响，并探讨R-环的三维几何结构。本项目的目标是通过以下三个具体目标来阐明引导R-环起始、延伸、终止和最终解离的序列和拓扑与空间约束：（1）实验性地剖析DNA序列对R-环形成的影响，并利用这些发现来发展模拟和预测R-环出现的辫子语法;（2）揭示DNA拓扑结构在调节R环形成中的作用，并描述其3D结构;（3）开发基于辫子语法和有向图的数学技术，以探索R环形成的动力学。除了解决关键的生物学问题，这项工作将产生新的数学知识，并有助于跨学科研究的新兴领域的发展。这个奖项反映了NSF的法定使命，并已被认为是值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估的支持。

Interactions of the two sister molecules of life, RNA and DNA, have long been a focus of scientific inquiry. A new molecular complex, known as an R-loop, consisting of a DNA duplex and an RNA strand was recently discovered. It has been found that R-loops are prevalent, and shown to be functionally important structures that are observed across the kingdom of life, from bacteria to mammals. R-loops are now understood to act as a new type of signal with important roles in a growing number of biological processes. Defects in R-loop formation have been implicated in disease in a wide variety of species including humans. However, little is currently understood about the formation and the structure of R-loops. This project will address the forces that control R-loop initiation, the way in which R-loops start and terminate, the geometry of the RNA-DNA complex, and the factors that dictate R-loop stability. This work will advance the fields of mathematics and biology while also reinforcing their mutual interconnections through blending theoretical approaches with experimental work. The research provides new avenues for postdoctoral, graduate and undergraduate training in experimental and mathematical biology and includes a mentoring component specifically by and for women mathematicians to support their scientific engagement and increase their visibility. The research findings will be disseminated broadly. R-loops are three-stranded structures composed of an RNA:DNA duplex and a single-strand of DNA. Initially found in bacteria, R-loops can account for 3-5% of the genome of yeasts, plants and mammals. This project uses novel mathematical approaches to examine the effects of DNA sequence and DNA topology on R-loop formation and to probe the three-dimensional geometry of R-loops. The goal of this project is to elucidate the sequence and the topological and spatial constraints that guide the initiation, elongation, termination, and ultimate dissociation of R-loops, through implementing the following three specific aims: (1) Experimentally dissect the influence of DNA sequence on R-loop formation and use these findings to develop braid grammars that model and predict the appearance of R-loops; (2) Uncover the role of DNA topology in regulating the formation of R-loops, and describe their 3D structure; and (3) Develop mathematical techniques based on braid grammars and directed graphs that probe the dynamics of R-loop formation. In addition to addressing key biological questions, the work will generate new mathematical knowledge and contribute to the development of an emergent area of interdisciplinary study.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.