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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 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.

SUBMITTER: Fortin JP

PROVIDER: S-EPMC4574526 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature

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

Fortin Jean-Philippe JP Hansen Kasper D KD

Genome biology 20150828

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 ...[more]

PMID: 26316348

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