Cells (10-20 x 10^6 cells) were crosslinked for 10min at 37C with 1% (vol/vol) formaldehyde, followed by quenching with 0.125 M glycine (final concentration). Crosslinked cell samples were then sonicated with a Covaris sonicator to obtain DNA fragments 200-300 bp in length. Samples were incubated with 5ug of anti-CTCF antibody (07-729, Millipore) overnight at 4C in RIPA buffer (10 mM Tris, pH 7.6, 1 mM EDTA, 0.1% (wt/vol) SDS, 0.1% (wt/vol) sodium deoxycholate and 1% (vol/vol) Triton X-100). Beads were washed twice with RIPA buffer, twice with RIPA buffer/300 mM NaCl, once with Wash buffer3 (250 mM LiCl, 0.5% (vol/vol) NP-40, 0.5% (vol/vol) deoxycholate, 1 mM EDTA and 10 mM Tris-HCl (pH 8.1)) and then once with TE (10 mM Tris-HCl (pH 7.5) and 1 mM EDTA) + 0.2% Triton and once with TE. ChIP DNA was then extracted for 4h at 65C in Tris-EDTA buffer with 0.3% (wt/vol) SDS and proteinase K (1 mg/ml). Library preparation follwed standard protocols.