All cells in an organism share the same genome but adopt remarkably different identities and functions because the genes they express differ. These differences are shaped by multiple layers of genomic regulation, including chromatin accessibility and three-dimensional (3D) genome organization.

Bulk chromosome conformation capture (3C) methods such as Hi-C have revealed a key role for the 3D genome in gene regulation but cannot resolve cellular heterogeneity within complex tissues. Existing single-cell 3C methods can resolve heterogeneity but cannot capture long-range enhancer–promoter interactions efficiently, have low throughput and are prohibitively costly, limiting their broad application. They also face challenges in simultaneously capturing high-quality transcriptome, chromatin accessibility and 3D genome features from the same cell. Instead, trimodal integration has to be computationally inferred from separate assays using different input cells, which lacks ground truth and often leads to inaccuracies.