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

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

Author information

1
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Road, Baltimore, 21205, MD, USA. fortin@jhsph.edu.
2
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Road, Baltimore, 21205, MD, USA. khansen@jhsph.edu.
3
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 1900 East Monument Street, Baltimore, 21205, MD, USA. khansen@jhsph.edu.

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.

PMID:
26316348
PMCID:
PMC4574526
DOI:
10.1186/s13059-015-0741-y
[Indexed for MEDLINE]
Free PMC Article

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