Molecular Mechanisms of Three-Dimensional Genome Architecture and Its Implications for Cancer

Chromatin is dynamically folded into a hierarchical three-dimensional (3D) genome architecture that plays essential roles in gene regulation, DNA replication, and genome stability. Chromosome conformation capture (3C)-based technologies, particularly Hi-C and Micro-C, integrate chromatin fragmentation, proximity ligation, and high-throughput sequencing to map genome-wide chromatin interactions and have greatly advanced our understanding of spatial genome organization. These approaches have revealed three major levels of chromatin architecture: chromatin compartments, topologically associating domains (TADs), and chromatin loops, enhancer-promoter (E-P) interactions are frequently constrained within TADs, providing a structural framework for precise transcriptional control. Key architectural proteins, including CCCTC-binding factor (CTCF), cohesin, and the Mediator complex, are central to the establishment and maintenance of chromatin loops and TAD boundaries. In addition, lineage-specific transcription factors contribute to the dynamic organization of chromatin and the regulation of gene expression in a tissue- and developmental stage-specific manner. Genomic structural variations (SVs), including deletions, duplications, inversions, translocations, and complex chromosomal rearrangements, can disrupt TAD boundaries, alter chromatin looping and E-P interactions, and rewire higher-order genome organization, thereby promoting tumor initiation and progression. In this review, we summarize major advances in understanding 3D genome architecture, discuss current models and molecular mechanisms of chromatin folding, review chromatin interaction technologies, and highlight emerging links among structural genome variation, architectural protein dysfunction, chromatin dysregulation, and cancer development.