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

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 be reliably estimated using epigenetic data from several different platforms, the Illumina 450k DNA methylation microarray, DNase hypersensitivity sequencing, single-cell ATAC sequencing and single-cell whole-genome bisulfite sequencing. We do this by exploiting the fact that the structure of long range correlations differs between open and closed compartments. This work makes A/B compartments readily available in a wide variety of cell types, including many human cancers.