Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics (cell-line)

Single-cell three-dimensional (3D) genome techniques have advanced our understanding of cell-type-specific chromatin structures in complex tissues, yet current methodologies are limited in cell throughput. Here we introduce a high-throughput single-cell Hi-C approach (dscHi-C) and its transcriptome co-assay (dscHi-C-multiome) using droplet microfluidics. Using dicHi-C, we investigated chromatin structural changes during mouse brain aging by profiling 32,777 single cells across three developmental stages (3 month, 12 month and 23 month), yielding a median of 78,220 unique contacts. Our results show that genes with significant structural changes are enriched in pathways related to metabolic process and morphology change in neurons, and innate immune response in glial cells, highlighting the role of 3D genome organization in physiological brain ageing. Furthermore, our multi-omics joint assay, dscHi-C-multiome, enables precise cell type identification in the adult mouse brain and uncovers the intricate relationship between genome architecture and gene expression. Collectively, we developed the sensitive, high-throughput dscHi-C and its multi-omics derivative, dscHi-C-multiome, demonstrating their potential for large-scale cell atlas studies in development and disease. In this study, we performed droplet-based single-cell Hi-C (dscHi-C) and its transcriptome co-assay (dscHi-C-multiome) on human and mouse cell line, and mouse brain cortex tissues.