Single-cell multiomic methods for studying genome structure and function

研究基因组结构和功能的单细胞多组学方法

• 批准号: 10884769
• 负责人: Zhijun Duan
• 金额: $ 40万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-09 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10884769
• 关键词: 3-Dimensional; Architecture; Automobile Driving; Benchmarking; Biological; Biological Assay; Biology; Cell Differentiation process; Cell Nucleus; Cells; Chromatin; Chromatin Loop; Chromatin Structure; Clinical; Communities; Complex; Coupled; Cues; DNA biosynthesis; Dependence; Development; Developmental Process; Disease; Distal; Enhancers; Epigenetic Process; Gene Expression; Gene Expression Regulation; Genetic Transcription; Genome; Genomics; Goals; Health; Hi-C; Human; Hybrids; Image; In Situ; Individual; Investigation; Joints; Location; Maps; Measurement; Measures; Methods; Modality; Molecular; National Human Genome Research Institute; Nuclear; Organ; Outcome; Pathogenesis; Phenotype; Pilot Projects; Play; Policies; Property; Protocols documentation; Public Health; Regulatory Element; Research; Resolution; Role; Signal Transduction; Structure; Structure-Activity Relationship; Technology; Technology Transfer; Tissues; Transcriptional Regulation; Variant; Work; computerized tools; epigenomics; genome-wide; genomic tools; machine learning algorithm; mammalian genome; multiple omics; new technology; novel; programs; promoter; single-cell RNA sequencing; spatial integration; spatiotemporal; tool; transcriptome; transcriptomics; tumorigenesis; whole genome

PROJECT SUMMARY The three-dimensional (3D) genome organization in the nucleus is pivotal to various genome functions such transcription and DNA replication. Recent development in both genomic and imaging-based technologies has drastically advanced our understanding of the multiscale 3D genome structures and their variability in single cells. However, although methods can separately map transcriptome (e.g., single-cell RNA-seq) or 3D genome (e.g., single-cell Hi-C), no technology exists to map both 3D genome and transcriptome in the same cells, significantly limiting the investigation of the relationship between genome structure and function at the single-cell level. For example, without such a co-assayed method, it remains infeasible to study how 3D genome architecture functionally informs spatiotemporal transcriptional rewiring in single cells in developmental processes. To fill this major gap in the field of single-cell epigenomics, this project will develop new technologies for quantitatively comparing 3D genome and gene expression in the same single cells. We will develop CARE- seq, a novel single-cell multiomic solution, coupled by our state-of-the-art computational tools, to unveil the connections between 3D genome organization and gene expression as well as their spatial and temporal variations. (1) We will develop the first co-assayed method to jointly measure whole-genome chromatin interactions and gene expression in the same single cells from complex tissues in a massively parallel manner. (2) We will develop a new method to concurrently profile single-cell transcriptome and specific promoter- enhancer loops in thousands of individual cells. (3) We will further combine spatial biology with our single-cell method to develop a spatially resolved approach for deciphering in situ dynamics of both 3D genome and gene expression in single-cell resolution for tissues. Collectively, the new technologies developed in this project will provide unprecedented new opportunities to systematically understand the interplay between 3D genome structure and transcriptional regulation for a wide range of biological contexts.

项目摘要 细胞核中的三维（3D）基因组组织对于各种基因组功能是关键的， 转录和DNA复制。基因组和基于成像的技术的最新发展 极大地推进了我们对多尺度3D基因组结构及其在单个基因组中的变异性的理解。 细胞然而，尽管方法可以单独地映射转录组（例如，单细胞RNA-seq）或3D基因组 (e.g.,单细胞Hi-C），没有技术可以在同一细胞中绘制3D基因组和转录组， 这大大限制了对单细胞基因组结构和功能之间关系的研究， 水平例如，如果没有这样的共测定方法，研究3D基因组如何在细胞中表达仍然是不可行的。 结构功能上通知时空转录重新布线在单细胞发育 流程.为了填补单细胞表观基因组学领域的这一重大空白，本项目将开发新技术 用于定量比较相同单细胞中的3D基因组和基因表达。我们将继续关注- seq，一种新的单细胞多组学解决方案，加上我们最先进的计算工具，揭示了 三维基因组组织和基因表达之间的联系，以及它们的空间和时间 变化. (1)我们将开发第一个联合测定全基因组染色质的方法 以大规模平行的方式在来自复杂组织的相同单细胞中进行相互作用和基因表达。 (2)我们将开发一种新的方法，同时分析单细胞转录组和特异性启动子- 成千上万个细胞中的增强环。(3)我们将进一步将联合收割机空间生物学与我们的单细胞 一种开发空间分辨方法的方法，用于破译3D基因组和基因的原位动力学 以组织的单细胞分辨率表达。总的来说，该项目开发的新技术将 为系统地了解3D基因组之间的相互作用提供了前所未有的新机会， 结构和转录调控的广泛的生物背景。