HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution

摘要

Cells are complex, dynamic environments that require constant regulation of their genes to ensure survival. The advent of chromosome conformation capture (3C) technologies [ ], and recent advances in imaging techniques [ ], have led to an improved understanding of genome organization and its role in gene regulation [ , ]. Hi-C [ ], a high-throughput derivative of 3C, provides an unparalleled view of three-dimensional (3D) genome organization by capturing all DNA-DNA contacts found within a population of cells. Hi-C has revealed different levels of genome organization, including the topologically associating domains (TADs [ , ], subTADs [ , ]), and chromatin compartments [ ]. Yet, the potential for a more refined understanding of 3D genome organization remains largely untapped [ ].