Single-cell multiomic methods for studying genome structure and function

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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.