A method to recognize universal patterns in genome structure using Hi-C

The expression of genes in cells is a complicated process. Expression levels of a gene are determined not only by its local neighborhood but also by more distal regions, as is the case with enhancer-promoter interactions, which can connect regions millions of bases away [1]. The large-scale organization of DNA within the cell nucleus plays a substantial role in gene expression and cell fate, with recent developments in biochemical assays (such as Hi-C) generating quantitative maps of the higher-order structure of DNA. The interactions captured by Hi-C have been attributed to several distinct physical processes. One of the processes is that of segregation of DNA into compartmental domains by phase separation. While the current consensus is that there are broadly two types of compartmental domains (A and B), there is some evidence for a larger number of compartmental domains [2]. Here a methodology to determine the identity and number of such compartments is presented, and it is observed that there are four distinct compartments within the genome.