For ChIP-Seq, nuclear lysates were sonicated and Ctcf-DNA complexes were isolated with Ctcf antibody (Millipore, 07-729). Libraries of purified DNA were generated using Illumina SR adapters (Illumina) following manufacturer’s manual, and were selected for the inserted fragments of 200 ± 50 bp, and sequenced 36 bases on an Illumina Genome Analyzer II.