A cartoon illustrating the various constitutive binding sites. The blue, orange, and green horizontal bars represent the 200 bp ChIP-seq peaks for CTCF, Rad21, and Smc3 proteins, respectively. There were 56, 6, and 4 human cell lines for which CTCF, Rad21, and Smc3 ChIP-seq data were available. We first predicted the CTCF binding site in the peaks, represented by the black rectangles (see Method). We define as a “constitutive” CTCF site any CTCF binding site found in more than 90% of the cell lines. We use ‘c’ in front of a protein to indicate constitutive, ‘/’ between proteins to indicate co-localization/overlap. A cRad21 site that overlaps with a cSmc3 site is referred to as a cRad21/cSmc3 or cCohesin site, similarly for cCTCF/cCohesin sites.
Li et al. BMC Genomics 2013 14:553 doi:10.1186/1471-2164-14-553