Cells harvested from 100 mm dishes were cross-linked with 1% formaldehyde for 15 minutes at room temperature and cross-linking was quenched with 125 mM glycine. After lysing cells in buffer containing detergents (1% Triton X-100, 0.5% sodium deoxycholate, 1% SDS, 10 mM EDTA, 50 mM Tris-Cl [pH 8.0]), the chromatin was sonicated to an average length of 300 bp by 30% pulses at a 10 seconds interval, repeated 30 times, and then immunoprecipitated overnight using an anti-CTCF antibody (Cell Signaling Technology). Sequencing libraries were manually generated for high-throughput sequencing. Either end of DNA strands was filled using the Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI). Adenine was added at 3’ ends by Taq DNA polymerase (New England Biolabs, Beverly, MA) under dATP conditions. Illumina’s adaptor oligomers was ligated at both ends using Quick Ligation kit (Qiagen, Germantown, MD). After purified twice, DNA libraries are amplified using Solexa primers (Illumina, San Diego, CA) and Phusion PCR master mix (Thermo Scientific, Hudson, NH).