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

该项目将通过吸引定量生物学前沿领域的研究生、本科生和高中生，阐明3D基因组组织在基因调控过程中的作用。适当的基因调控对各种细胞功能的顺利执行至关重要。事实上，在错误的地方或错误的发育阶段过多或过少的基因表达往往会导致发育缺陷。除了调控元件与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起着重要作用。该项目的总体目标是表征早期果蝇胚胎中三维基因组组织受到扰动时确保正常发育的基因表达的时空范围。为加强学生对定量生物学跨学科研究的参与，将设立一个定量生物学的本科生设计项目和一个面向高中生的虚拟拓展计划。最近各种“seq”技术的发展通过提供增强子-启动子相互作用和基因活性的全基因组视角，推动了转录调控领域的发展。然而，目前尚不清楚的是，在给定的细胞中，结构蛋白、增强子和启动子的特定排列应该维持多长时间或保持多紧密才能导致适当的基因表达。这个问题将通过追踪单个活细胞中染色质组织和转录活性的动态变化来解决。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在早期果蝇胚胎中使用，以检查基因组拓扑结构和基因活性的结构-功能关系。具体来说，远程增强子-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本项目中得到表征。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。

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.