Network models of chromatin structure

Increasing numbers of datasets and experimental assays that capture the organization of chromatin inside the nucleus warrant an effort to develop tools to visualize and analyze these structures. Alongside polymer physics or constraint-based modeling, network theory approaches to describe 3D epigenome organization have gained in popularity. Representing genomic regions as nodes in a network enables visualization of 1D epigenomics datasets in the context of chromatin structure maps, while network theory metrics can be used to describe 3D epigenome organization and dynamics. In this review, we summarize the most salient applications of network theory to the study of chromatin contact maps, demonstrating its potential in revealing epigenomic patterns and relating them to cellular phenotypes.

Automated summary

With the increasing availability of datasets and experimental assays on chromatin organization, there is a need for tools to visualize and analyze these structures. Network theory approaches have become popular for describing 3D epigenome organization, enabling visualization of 1D epigenomics datasets and analysis of 3D organization and dynamics. This review summarizes the applications of network theory in studying chromatin contact maps and highlights its potential in uncovering epigenomic patterns and their relationship to cellular phenotypes.