4 x 106 TKO or WT mESCs were harvested and fixed as described in the Hi-C method section. The crosslinked cells were resuspended in Nucleus/Chromatin Preparation (NCP) buffer I [10 mMHepes, pH 6.5, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100 and 1x protease inhibitors (Roche)] and incubated at 4oC for 10 min with gentle rotation. The suspension was centrifuged at 2,000g for 5 min. The pellets were resuspended in NCP buffer II (10 mM Hepes, pH 6.5, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 1x protease inhibitors), followed by centrifugation. The pellets were resuspended in SDS lysis buffer (10 mM Tris, pH 8.0, 1 mM EDTA, 1% SDS and 1x protease inhibitors). The suspension was sonicated with a Bioruptor sonicator (Diagenode) to break chromatin DNA into about 200 bp in size. The sonicated DNA was diluted 10-fold with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris, pH 8.1, and 167 mM NaCl). To precipitate chromatin, 40 μl protein A-Dynabeads (Life Technologies, 10001D) resuspended in 0.5 ml ChIP binding buffer (0.01% Tween-20 in 1x PBS) were incubated with 4 mg of antibodies for each IP at 4oC for 6 h. After washing with ChIP binding buffer, the beads were incubated with diluted sonicated chromatin DNA suspension overnight, continuously rotating. The beads were sequentially washed with low salt wash buffer (20 mM Tris pH 8.1, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, and 150 mM NaCl), high salt wash buffer (20 mM Tris pH 8.1, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, and 500 mM NaCl), LiCl buffer (10 mM Tris, pH8.0, 250 mM LiCl, 1% IGEPA CA630 (NP40), 1% Sodium deoxycholate, and 1 mM EDTA), and TE buffer. To reverse crosslinking, the beads were incubated with elution buffer (10 mM Tris, pH 8.0, 1% SDS, 1 mM EDTA and 0.2 mg/μl Proteinase K) at 65oC overnight. Supernatant was collected, extracted with Phenol:Chloroform (1:1), and precipitated with ethanol. The pellets were washed with 75% ethanol, air-dried and resuspended in 10 mM Tris (pH 8.0). DNA concentration was determined with a Quant-iTDS DNA kit (Life Tech, Q-33120). 1 ~ 400 ng of DNA were used to prepare ChIP-seq libraries with a TruSeq DNA prep kit (Illumina) according to the manufacturer’s recommendation