NSF-ANR: Detailed and Mechanistic Characterization of TAD Boundaries Using Complementary Single-Molecule Sequencing and Super-Resolution Imaging Approaches

NSF-ANR：使用互补单分子测序和超分辨率成像方法对 TAD 边界进行详细和机械表征

• 批准号: 2207050
• 负责人: Eric Joyce
• 金额: $ 32.5万
• 依托单位: University of Pennsylvania
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-02-01 至 2025-01-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2207050&HistoricalAwards=false
• 关键词: NSF; ANR; Detailed; Mechanistic; Characterization

Eukaryotic genomes encode genetic information in their linear sequence, but appropriate expression of genes requires chromosomes to fold into complex and spatially distinct three-dimensional structures. Despite the remarkable conservation of these organizational features, there is limited understanding of how they enable chromosome function. A major leap forward in linking genome structure to function has been the discovery of Topologically Associating Domains (TADs), which are regional units of mammalian genomes implicated in gene regulation as well as DNA replication, repair and recombination. The boundaries between TADs are thought to prevent the “spreading” of molecular machineries involved in various processes. This research project aims to clarify the complex nature of TAD boundaries and better understand how they enable TAD structure and function. The project will also offer cross-disciplinary training opportunities for graduate and undergraduate students in complementary experimental and bioinformatic methods.Current experimental and in-silico models for TAD formation include simplified TAD boundaries consisting of punctuated and stable binding of CTCF protein. In contrast, recent evidence indicates that the boundaries are extended, dynamic and exhibit cell-to-cell variability. This project will employ novel single-molecule genomics approaches coupled with super-resolution imaging to identify and quantify the genetic elements that insulate neighboring TADs in single cells. The outcomes can help update models of TAD formation and improve understanding and prediction of how the boundaries contribute to TAD structure, dynamics and function. This new knowledge could in turn help identify mechanisms whereby uncharacterized genetic elements (e.g., identified in GWAS studies) cause subtle changes to gene regulation, DNA replication, repair and recombination. It may also help explain how TAD structure can be reorganized upon inherited or acquired changes to the non-coding genome (e.g., structural variation, polymorphisms).This collaborative US/France project is supported by the US National Science Foundation and the French Agence Nationale de la Recherche, where NSF funds the US investigator and ANR funds the partners in France.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.

真核基因组在其线性序列中编码遗传信息，但基因的适当表达需要染色体折叠成复杂和空间不同的三维结构。尽管对这些组织特征进行了显着的保护，但对它们如何启用染色体功能的理解有限。将基因组结构与功能联系起来的主要飞跃是发现了拓扑关联的域（TADS），这些结构域是基因调节中实施的哺乳动物基因组的区域单位，以及DNA复制，修复和重组。 TAD之间的边界被认为可以防止参与各种过程的分子机器的“扩散”。该研究项目旨在阐明TAD边界的复杂性质，并更好地了解它们如何实现TAD结构和功能。该项目还将在完整的实验和生物信息学方法中为研究生和本科生提供跨学科培训机会。促成的实验性和silico模型的TAD形成模型包括由CTCF蛋白的稳定和稳定的结合组成的简化TAD界限。相反，最近的证据表明边界是扩展，动态和暴露的细胞间变异性的。该项目将采用新型的单分子基因组学方法，再加上超分辨率成像，以识别和量化单个细胞中相邻TAD的遗传元件。结果可以帮助更新TAD形成的模型，并提高对边界如何促进TAD结构，动态和功能的理解和预测。这种新知识反过来可能有助于确定机制，从而使未表征的遗传因素（例如，在GWAS研究中鉴定）会导致基因调节，DNA复制，修复和重组的细微变化。它还可能有助于解释如何在对非编码基因组的继承或获得更改（例如结构变化，多态性，多态性）的变化后如何重组TAD结构。该协作美国/法国项目得到了美国国家科学基金会的支持，并得到了法国国家科学基金会和法国Agence Nationale de la recherche的支持使用基金会的知识分子优点和更广泛的审查标准，被认为值得通过评估来支持。