CAREER: Imaging enhancer-mediated transcriptional regulation in 3D genome

这个项目将通过让研究生、本科生和高中生参与到数量生物学的前沿领域来阐明3D基因组组织在发育过程中的基因调控中的作用。适当的基因调控对于各种细胞功能的顺利执行至关重要。事实上，在错误的位置或错误的发育阶段表达过多或过少的基因往往会导致发育缺陷。除了调控元件和靶基因之间的直接相互作用外，DNA聚合物的折叠结构在基因调控中也起着重要的作用。该项目的总体目标是表征基因表达的空间和时间范围，以确保在3D基因组组织扰动时早期果蝇胚胎的正常发育。将建立数量生物学本科生设计项目和面向高中生的虚拟推广计划，以加强学生对数量生物学跨学科研究的参与。各种“序列”技术的最新发展为转录调控领域提供了一个全基因组视角的增强子-启动子相互作用和基因活性。然而，目前尚不清楚在特定细胞中，特定的结构蛋白、增强子和启动子的排列应该维持多长时间或多近才能导致适当的基因表达。这个问题将通过跟踪单个活细胞中染色质组织和转录活动的动态变化来解决。包括基因组编辑、定量实时成像和数学建模在内的多种方法将被应用于果蝇早期胚胎，以研究基因组拓扑和基因活性的结构-功能关系。具体地说，长程增强子-启动子相互作用和等位基因间的关联将受到干扰，对转录动力学的影响将在这个项目中得到表征。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

This project will elucidate the role of 3D genome organization in gene regulation during development by engaging graduate, undergraduate, and high school students in the cutting-edge field of quantitative biology. Proper gene regulation is crucial for the smooth execution of various cellular functions. Indeed, too much or too little gene expression in the wrong place or at the wrong developmental stages often leads to developmental defects. The folded structure of the DNA polymer plays an important role in gene regulation, in addition to direct interactions between regulatory elements and the target gene. The overall goal of the project is to characterize the spatial and temporal range of gene expression that ensures normal development upon perturbation of 3D genome organization in early Drosophila embryos. An undergraduate design project in quantitative biology and a virtual outreach program for high school students will be established to enhance students’ involvement in interdisciplinary research in quantitative biology. The recent development of various “seq” techniques have advanced the field of transcriptional regulation by providing a genome-wide perspective of enhancer-promoter interactions and gene activity. However, it is still unclear how long or how closely a specific arrangement of architecture proteins, enhancers, and promoters in a given cell should be maintained to result in proper gene expression. This question will be addressed by tracking dynamic changes in chromatin organization and transcriptional activity in individual living cells. Multiple approaches, including genome editing, quantitative live imaging and mathematical modeling will be employed in early Drosophila embryos to examine the structure-function relationships of genome topology and gene activity. Specifically, long-range enhancer-promoter interactions and inter-allelic associations will be perturbed and the effects on transcriptional dynamics will be characterized in this project.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.