Navigating the 3D genome at single-cell resolution: techniques, computation, and mechanistic landscapes

The 3D organization of the genome is critical for gene expression regulation, cellular identity, and disease progression. Traditional methods that analyze bulk genomic data often obscure cell-to-cell heterogeneity, limiting the resolution of intrinsic variability within complex biological systems. To overcome this, single-cell 3D genomics has emerged, revealing chromatin architecture at the individual cell level. Advanced experimental approaches enable genome-wide chromatin contact mapping, while computational frameworks reconstruct dynamic chromatin topologies from high-dimensional data. Building on these breakthroughs, recent advances in single-cell 3D genomics have led to transformative progress in epigenetics, linking 3D genome architecture with gene regulation, cellular identity, and disease phenotypes. This review focuses on the breakthroughs in single-cell 3D genomics, demonstrating how integrated experimental, computational, and mechanistic approaches decode chromatin architecture. These insights have deepened the understanding of genome function at the single-cell level and lay the foundation for future advances in precision medicine and topology-guided therapeutic strategies.