Single-cell multiomic methods for studying genome structure and function

项目总结 细胞核中的三维(3D)基因组组织是各种基因组功能的关键，如 转录和DNA复制。基因组和基于成像的技术的最新发展已经 极大地提高了我们对多尺度3D基因组结构及其在单个 细胞。然而，尽管方法可以分别绘制转录组(例如，单细胞RNA-seq)或3D基因组 (例如，单细胞Hi-C)，不存在在同一细胞中映射3D基因组和转录组的技术， 极大地限制了单细胞基因组结构和功能之间关系的研究 水平。例如，如果没有这样的共同检测方法，研究3D基因组如何 结构在发育过程中对单细胞时空转录重连的功能信息 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3D基因组和基因在相同单细胞中的表达。我们将发展关爱- SEQ，一种新颖的单细胞多组体解决方案，结合我们最先进的计算工具，揭开了 三维基因组组织与基因表达及其时空关系的研究 变种。(1)我们将建立第一个联合检测全基因组染色质的方法 在来自复杂组织的同一单个细胞中以大规模平行的方式相互作用和基因表达。 (2)我们将开发一种新的方法来同时分析单细胞转录组和特定的启动子- 增强子在数千个单独的细胞中循环。(3)我们将进一步将空间生物学与我们的单细胞 开发一种空间分辨的方法来破译3D基因组和基因的原位动态 以单细胞分辨率表达组织。总体而言，该项目开发的新技术将 为系统了解3D基因组之间的相互作用提供了前所未有的新机会 广泛的生物学背景下的结构和转录调控。

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.