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

Genome Biol. 2015 Aug 28;16(1):180. doi: 10.1186/s13059-015-0741-y.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition
  • Chromatin / chemistry*
  • DNA / chemistry
  • DNA Methylation*
  • Epigenesis, Genetic*
  • Genomics
  • Humans
  • Male
  • Mutation Rate
  • Oligonucleotide Array Sequence Analysis
  • Prostatic Neoplasms / genetics
  • Sequence Analysis, DNA


  • Chromatin
  • DNA