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.

真核基因组以线性序列编码遗传信息，但基因的适当表达需要染色体折叠成复杂且空间上不同的三维结构。尽管这些组织特征得到了显着的保护，但人们对它们如何实现染色体功能的了解还很有限。连接基因组结构与功能的重大飞跃是拓扑关联域 (TAD) 的发现，它是哺乳动物基因组的区域单位，涉及基因调控以及 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。该项目还将为研究生和本科生提供互补实验和生物信息学方法的跨学科培训机会。当前 TAD 形成的实验和计算机模型包括简化的 TAD 边界，该边界由 CTCF 蛋白的间断和稳定结合组成。相比之下，最近的证据表明，边界是扩展的、动态的，并且表现出细胞间的变异性。该项目将采用新颖的单分子基因组学方法与超分辨率成像相结合，来识别和量化单细胞中隔离相邻 TAD 的遗传元件。研究结果有助于更新 TAD 形成模型，并提高对边界如何影响 TAD 结构、动力学和功能的理解和预测。这些新知识反过来可以帮助识别未表征的遗传元件（例如在 GWAS 研究中识别的）引起基因调控、DNA 复制、修复和重组的微妙变化的机制。它还可能有助于解释 TAD 结构如何根据非编码基因组的遗传或后天变化（例如结构变异、多态性）进行重组。这个美国/法国合作项目得到了美国国家科学基金会和法国国家研究机构的支持，其中 NSF 资助美国研究人员，ANR 资助法国合作伙伴。该奖项反映了 NSF 的法定使命，并具有 通过使用基金会的智力优点和更广泛的影响审查标准进行评估，被认为值得支持。