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

Jean Philippe Fortin, Kasper D. Hansen

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number180
JournalGenome biology
Volume16
Issue number1
DOIs
StatePublished - Aug 28 2015

Keywords

  • Chromatin
  • Chromosome configuration capture
  • DNase sequencing
  • Epigenetics
  • Hi-C
  • Methylation
  • Single-cell

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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