Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data
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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 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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Distributions of replication timing and open/closed chromatin compartment calls from TCGA data corroborated the data of the annotated domains.
“Furthermore, distributions of replication timing for various cell types and open/closed chromatin compartment calls from TCGA data37 corroborated the data of the annotated domains (Extended Data Fig. 7d,e).”
From Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) · cites this paper as [37]
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- Authors
- Fortin, J.-P., & Hansen, K. D.
- Affiliations
- Johns Hopkins University (US)
- Corresponding author
- Hansen, Kasper D.
- ORCID
- Hansen, Kasper D.
- Venue
- Genome Biology
- Published
- 2015-08-28
- Volume
- 16
- Issue
- 1
- Pages
- 180-180
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC4574526
- OpenAlex
- W1896708637
- Cited by
- 333
- References
- 50
- Citations by year
- 2026: 14 · 2025: 24 · 2024: 45 · 2023: 46 · 2022: 42 · 2021: 42 · 2020: 34 · 2019: 34 · 2018: 19 · 2017: 19 · 2016: 11 · 2015: 2 · 2014: 1
- FWCI
- 7.39
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genome biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- A/B compartments, 3D genome organization, long-range correlations, chromatin accessibility, DNA methylation, DNase hypersensitivity, ATAC-seq, bisulfite sequencing, tumor cell types
- MeSH terms
- Base Composition, Chromatin, DNA, Humans, Male, Prostatic Neoplasms, Sequence Analysis, DNA, DNA Methylation, Oligonucleotide Array Sequence Analysis, Genomics, Epigenesis, Genetic, Mutation Rate
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