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 核中的三维（3D）基因组组织与各种基因组功能至关重要 转录和DNA复制。基于基因组和基于成像的技术的最新发展具有 我们对多尺度3D基因组结构的理解及其单一的变异性急剧提高了我们的理解 细胞。但是，尽管方法可以单独映射转录组（例如单细胞RNA-SEQ）或3D基因组 （例如，单细胞HI-C），在同一细胞中绘制3D基因组和转录组的技术不存在 显着限制了单细胞基因组结构与功能之间关系的研究 等级。例如，没有这样的共同方法，研究3D基因组如何仍然是不可行的 架构在功能上为发育中的单个细胞中的时空转录重新布线提供信息 过程。为了填补单细胞表观基因组学领域的这一主要空白，该项目将开发新技术 用于定量比较同一单个细胞中的3D基因组和基因表达。我们将发展关怀 - SEQ是一种新型的单细胞多组分解决方案，与我们最先进的计算工具相结合，以揭露 3D基因组组织与基因表达以及它们的空间和时间之间的联系 变化。 （1）我们将开发第一种共同测定的方法来共同测量全基因组染色质 相互作用和基因表达以大量平行的方式来自复杂组织的同一单个细胞。 （2）我们将开发一种新方法，以同时介绍单细胞转录组和特定启动子 - 增强子循环在数千个单个单元中。 （3）我们将进一步将空间生物学与单细胞结合 开发一种空间解决方法来解密3D基因组和基因的原位动力学的方法 在组织单细胞分辨率中的表达。总的来说，该项目开发的新技术将 提供前所未有的新机会，以系统地了解3D基因组之间的相互作用 各种生物环境的结构和转录调节。