# Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data

## TL;DR

This paper shows how to estimate A/B compartments in the genome using various epigenetic data, making it easier to study chromatin structure in many cell types.

## Contribution

A novel method to reconstruct A/B compartments using long-range correlations in epigenetic data across multiple platforms.

## Key findings

- A/B compartments can be reliably estimated using epigenetic data from multiple platforms.
- Long-range correlations in epigenetic data differ between open and closed chromatin compartments.
- The method is applicable to a wide range of cell types, including human cancers.

## Abstract

Analysis of Hi-C data has shown that the genome can be divided into two compartments called A/B compartments. These compartments are cell-type specific and are associated with open and closed chromatin. We show that A/B compartments can reliably be estimated using epigenetic data from several different platforms: the Illumina 450 k DNA methylation microarray, DNase hypersensitivity sequencing, single-cell ATAC sequencing and single-cell whole-genome bisulfite sequencing. We do this by exploiting that the structure of long-range correlations differs between open and closed compartments. This work makes A/B compartment assignment readily available in a wide variety of cell types, including many human cancers.

The online version of this article (doi:10.1186/s13059-015-0741-y) contains supplementary material, which is available to authorized users.