The paper introduce scHiCAR, a high-throughput and cost-effective multiomic technology designed to simultaneously profile the transcriptome, epigenome, and 3D genome within individual cells. This plate-based method utilizes combinatorial barcoding to integrate data on mRNA, open chromatin, and chromosome conformation, specifically enriching long-range interactions anchored at cis-regulatory elements. Researchers successfully applied this tool to over 1.6 million mouse brain cells, revealing complex gene-regulatory landscapes across 22 distinct cell types. To enhance data analysis, the authors developed scDeepLUCIA, a deep-learning-based loop caller that identifies high-resolution chromatin interactions even in rare cell populations with low sequencing depth. Ultimately, scHiCAR provides a scalable framework for studying how three-dimensional genome reorganization influences transcriptional control in heterogeneous tissues and biological processes like muscle regeneration.

References:

• Wei X, Xu Y, Yang D, et al. Trimodal single-cell profiling of transcriptome, epigenome and 3D genome in complex tissues with scHiCAR[J]. Nature biotechnology, 2026: 1-16.