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

Jean-Philippe Fortin, View ORCID ProfileKasper D. Hansen
doi: https://doi.org/10.1101/019000
Jean-Philippe Fortin
1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
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Kasper D. Hansen
1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
2McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine
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  • ORCID record for Kasper D. Hansen
  • For correspondence: khansen@jhsph.edu
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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 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 03, 2015.
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Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data
Jean-Philippe Fortin, Kasper D. Hansen
bioRxiv 019000; doi: https://doi.org/10.1101/019000
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Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data
Jean-Philippe Fortin, Kasper D. Hansen
bioRxiv 019000; doi: https://doi.org/10.1101/019000

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