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

Fortin JP, Hansen KD - Genome Biol. (2015)

Bottom Line: 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 do this by exploiting that the structure of long-range correlations differs between open and closed compartments.

View Article: PubMed Central - PubMed

Affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Road, Baltimore, 21205, MD, USA. fortin@jhsph.edu.

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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Densities of the correlations of DNase data. Chromosome 14 was binned at resolution 100 kb. Depicted are the correlations of these data for the DNase-EBV dataset, stratified by compartment type. The open and closed compartments were defined using the HiC-EBV-2014 dataset. a The correlations without GC content correction. b The correlations after GC content correction. This figure is similar to Fig. 4
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Fig15: Densities of the correlations of DNase data. Chromosome 14 was binned at resolution 100 kb. Depicted are the correlations of these data for the DNase-EBV dataset, stratified by compartment type. The open and closed compartments were defined using the HiC-EBV-2014 dataset. a The correlations without GC content correction. b The correlations after GC content correction. This figure is similar to Fig. 4

Mentions: To examine why the correlation-based approach works for DNase data, we performed the same investigation as for the 450 k datasets. In Fig. 15, we show the distribution of correlations stratified by compartment type. As for the DNA methylation data, the DNase data have high positive correlations between bins in the closed compartment, although the correlations in the DNase data are much higher. For DNA methylation data, correlations were close to zero between loci when at least one locus was in the open compartment. In contrast, the DNase data show an almost uniform distribution of correlation values when one of the two loci are in the open compartment. In the same figure, we display the distribution of correlations when we used a sample-specific GC content effect correction; this correction changes the correlation substantially and suggests that some of the correlation structure is driven by GC content. Nevertheless, correcting for this effect slightly decreased our power to estimate the Hi-C compartments.Fig. 15


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

Fortin JP, Hansen KD - Genome Biol. (2015)

Densities of the correlations of DNase data. Chromosome 14 was binned at resolution 100 kb. Depicted are the correlations of these data for the DNase-EBV dataset, stratified by compartment type. The open and closed compartments were defined using the HiC-EBV-2014 dataset. a The correlations without GC content correction. b The correlations after GC content correction. This figure is similar to Fig. 4
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4574526&req=5

Fig15: Densities of the correlations of DNase data. Chromosome 14 was binned at resolution 100 kb. Depicted are the correlations of these data for the DNase-EBV dataset, stratified by compartment type. The open and closed compartments were defined using the HiC-EBV-2014 dataset. a The correlations without GC content correction. b The correlations after GC content correction. This figure is similar to Fig. 4
Mentions: To examine why the correlation-based approach works for DNase data, we performed the same investigation as for the 450 k datasets. In Fig. 15, we show the distribution of correlations stratified by compartment type. As for the DNA methylation data, the DNase data have high positive correlations between bins in the closed compartment, although the correlations in the DNase data are much higher. For DNA methylation data, correlations were close to zero between loci when at least one locus was in the open compartment. In contrast, the DNase data show an almost uniform distribution of correlation values when one of the two loci are in the open compartment. In the same figure, we display the distribution of correlations when we used a sample-specific GC content effect correction; this correction changes the correlation substantially and suggests that some of the correlation structure is driven by GC content. Nevertheless, correcting for this effect slightly decreased our power to estimate the Hi-C compartments.Fig. 15

Bottom Line: 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 do this by exploiting that the structure of long-range correlations differs between open and closed compartments.

View Article: PubMed Central - PubMed

Affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Road, Baltimore, 21205, MD, USA. fortin@jhsph.edu.

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.

Show MeSH
Related in: MedlinePlus