How do you study 3D genome organization and its functional implications?

3D genome organization is studied through chromosome conformation capture techniques: 3C (one-to-one), 4C (one-to-all), 5C (many-to-many), Hi-C (all-to-all genome-wide), and Micro-C (nucleosome resolution). Analysis reveals hierarchical organization: chromosome territories, A/B compartments (active/inactive), topologically associating domains (TADs), and chromatin loops. TAD boundaries often contain CTCF and cohesin. Integration with ChIP-seq, ATAC-seq, and expression data links structure to function. Enhancer-promoter loops within TADs regulate gene expression. Disruption of TAD boundaries can cause developmental disorders (limb malformations) and cancer by enabling aberrant enhancer-promoter contacts. Imaging approaches (FISH, live-cell imaging) complement sequencing methods for validation.