Identification of hierarchical chromatin domains.

ABSTRACT:

Motivation

The three-dimensional structure of the genome is an important regulator of many cellular processes including differentiation and gene regulation. Recently, technologies such as Hi-C that combine proximity ligation with high-throughput sequencing have revealed domains of self-interacting chromatin, called topologically associating domains (TADs), in many organisms. Current methods for identifying TADs using Hi-C data assume that TADs are non-overlapping, despite evidence for a nested structure in which TADs and sub-TADs form a complex hierarchy.

Results

We introduce a model for decomposition of contact frequencies into a hierarchy of nested TADs. This model is based on empirical distributions of contact frequencies within TADs, where positions that are far apart ha

SUBMITTER: Weinreb C 

PROVIDER: S-EPMC4892410 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature