title: 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.
authors: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Road, Baltimore, 21205, MD, USA. fortin@jhsph.edu.
authors: Jean-Philippe
authors: JP
authors: Fortin
authors: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Road, Baltimore, 21205, MD, USA. khansen@jhsph.edu.|McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 1900 East Monument Street, Baltimore, 21205, MD, USA. khansen@jhsph.edu.
authors: Kasper D
authors: KD
authors: Hansen
mesh_terms: D001482:Base Composition; D002843:Chromatin / Q000737:chemistry*; D004247:DNA / Q000737:chemistry; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D023281:Genomics; D006801:Humans; D008297:Male; D059645:Mutation Rate; D020411:Oligonucleotide Array Sequence Analysis; D011471:Prostatic Neoplasms / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D002843:Chromatin; D004247:DNA