The paper introduces scHiCAR, an innovative multiomics technology that simultaneously maps the transcriptome, epigenome, and 3D genome from individual cells. This method utilizes a plate-based combinatorial barcoding approach to achieve high throughput, allowing for the cost-effective analysis of millions of cells in a single experiment. Unlike previous techniques, scHiCAR excels at capturing long-range cis-regulatory interactions and open chromatin regions with high precision. Researchers successfully applied this tool to complex tissues, including the mouse brain and skeletal muscle, to define cell-type-specific gene regulation landscapes. To support this technology, the authors developed scDeepLUCIA, a deep-learning framework designed to identify high-resolution chromatin loops even in datasets with low cell numbers. Ultimately, the source highlights how scHiCAR provides a scalable system for understanding the structural and functional complexities of gene regulation in diverse biological environments.

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.