Sep 1, 2015

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

Genome Biology
Jean-Philippe Fortin, Kasper D Hansen

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.

  • References48
  • Citations31

Mentioned in this Paper

Hydrogen sulfite
DNA Methylation [PE]
Deoxyribonuclease I
Body Fluid Compartments
Genome
Neoplasms
DNA Methylation
Study of Epigenetics
Genomics
Sequencing

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