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

Banff International Research Station for Mathematical Innovation and Discovery

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 be reliably estimated using epigenetic data from several different platforms: the Illumina 450k DNA methylation microarray, DNase hypersensitivity sequencing, single- cell ATAC sequencing and single-cell whole-genome bisulfite sequencing. We do this by exploiting the fact that the structure of long range correlations differs between open and closed compartments. This work makes A/B compartments readily available in a wide variety of cell types, including many human cancers.

Mathematics; Statistics; Biology and other natural sciences

video/mp4

Author affiliation: Johns Hopkins University

2016-04-19

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/57679

Unreviewed

http://creativecommons.org/licenses/by-nc-nd/4.0/