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

基本信息

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
项目类别：
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

项目摘要

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.

项目概要细胞核中的三维 (3D) 基因组组织对于各种基因组功能至关重要，例如转录和DNA复制。基因组和成像技术的最新发展已经极大地增进了我们对多尺度 3D 基因组结构及其单基因组变异性的理解细胞。然而，尽管方法可以单独绘制转录组（例如单细胞 RNA-seq）或 3D 基因组图谱（例如，单细胞 Hi-C），不存在能够在同一细胞中同时绘制 3D 基因组和转录组图谱的技术，显着限制了单细胞基因组结构和功能之间关系的研究等级。例如，如果没有这样的联合测定方法，研究 3D 基因组如何进行分析仍然是不可行的。结构在功能上告知发育过程中单细胞的时空转录重连流程。为了填补单细胞表观基因组学领域的这一重大空白，该项目将开发新技术用于定量比较同一单细胞中的 3D 基因组和基因表达。我们将发展CARE- seq，一种新颖的单细胞多组学解决方案，与我们最先进的计算工具相结合，揭示了 3D 基因组组织和基因表达之间的联系及其空间和时间变化。 (1) 我们将开发第一个联合测定全基因组染色质的联合测定方法以大规模并行的方式研究来自复杂组织的相同单细胞中的相互作用和基因表达。 (2) 我们将开发一种同时分析单细胞转录组和特异性启动子的新方法- 数千个单个细胞中的增强子环。（3）我们将进一步将空间生物学与我们的单细胞结合起来开发一种空间分辨方法来破译 3D 基因组和基因的原位动力学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前所未有的新机会广泛的生物背景的结构和转录调控。