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Open Access Highly Accessed Research article

Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes

Yuanyuan Li1, Weichun Huang1, Liang Niu1, David M Umbach1, Shay Covo2 and Leping Li1*

Author Affiliations

1 Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA

2 Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University, Rehovot, Israel

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BMC Genomics 2013, 14:553  doi:10.1186/1471-2164-14-553

Published: 14 August 2013

Additional files

Additional file 1:

Supplementary Text.

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Additional file 2: Table S1:

Summary results for CTCF, Rad21, Smc3 and Znf143. Table S2. Comparison of the proportion of overlap (fraction of bins containing peaks for both proteins among bins containing peaks for at least one of the proteins) among constitutive sites versus non-constitutive sites. Table S3. Association between CTCF and Rad21/Smc3 and Rad21/Znf143 and Smc3/Znf143.

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Additional file 3: Figure S1:

The Venn diagrams showing the pair-wise overlap between CTCF and Rad21, Smc3, and Znf143 when both are constitutive or non-constitutive. Counts provide for each region in the Venn diagrams. Figure S2. The Venn diagrams showing the trio-wise overlap between CTCF and Rad21 and Smc3, Rad21 and Znf143, and Znf143 and Smc3 when both are constitutive or non-constitutive. Figure S3. Box plots of the fraction of overlap within each cell line between classes of CTCF sites and various factors/features. Figure S4. Density of epigenetic marks cCTCF/cCohesin loci (top panels, black) and the cCTCF-Cohesin loci (bottom panels, red) in Gm12878, Helas3, Hepg2, and K562 cell lines.

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Additional file 4:

Coordinates of constitutive CTCF binding sites.

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Additional file 5:

Coordinates of all unique CTCF binding sites identified in the 112 CTCF ChIP-seq datasets in 56 cell lines. The first three columns list the coordinates whereas the third column lists the strand in which the site was found. The last column lists the number of cell lines in which the site was identified. All coordinates are in GRCh37 build.

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