The three-dimensional (3D) organization of chromatin is a critical regulator of genome function across eukaryotes and is mediated by physical interactions between genomic loci that may be separated by a great distance along the linear genome. For example, millions of putative cis-regulatory elements have been identified, such as enhancers, with a great number of these found in intergenic regions thousands of kilobases away in linear sequence from neighboring genes. To obtain a more complete understanding of gene regulation, it is important to determine the 3D genome conformation and utilize this information to uncover the structural framework by which DNA chemical modifications, histone modifications, and chromatin binding proteins cooperate to orchestrate transcriptional regulation.
Hi-C is a proximity ligation method that captures long-range chromatin interactions across the genome, enabling researchers to uncover genome organizational structures such as chromatin compartments, topological domains (TADs), and chromatin loops. These structures all play important roles in gene regulation, such as providing a structural framework that confines local gene regulatory mechanisms and by providing a physical link between enhancers and their target genes – an integral component to the epigenetic mechanisms that regulate transcription.
By enabling genome-wide and targeted identification of 3D genome structures and promoter-enhancer looping, Hi-C has emerged as a powerful tool for refining our understanding of gene regulation within the 3D context of the genome and is widely used today in a variety of research areas and large-scale 3D genome mapping projects.