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.

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Datasets Mentioned

BETA
GM12878
GSE52025
GSE36369
GSE54882
GSE27146
GSE26133
GSE49629
GSE63525
GSE18199
GSE41763

Methods Mentioned

BETA
Hi-C
immunoprecipitation
chip
exome sequencing
ICE
WGBS

Software Mentioned

shinyMethyl
Maq
bedGraph
Hi
R
LOESS
Bowtie2
CGHub
rtracklayer
liftOver

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