70-80% confluent cells were fixed 10 minutes in 4% formaldehyde and stored at -80C. The pellets were subsequently resuspended in 1ml of ChIP-buffer [0.25% NP-40, 0.25% Triton X-100, 0.25% Sodium Deoxycholate, 0.005% SDS, 50nM Tris (pH8), 100mM NaCl, 5mM EDTA, 1X PMSF, 2mM NaF, 1X P8340 Cocktail Inhibitor (Roche)] and sonicated with a probe sonicator (Fisher Scientific Sonic Dismembrator Model 500) using the following cycles: 5 cycles at 20% power, 5 cycles at 25% power, and 5 cycles at 30% power. Each cycle lasts 10 seconds, and the samples are kept on ice between each cycle to avoid overheating. Next, the samples are spun at high speed in a microcentrifuge for 30 minutes. Then, lysates are collected and protein concentration measured using the Bradford assay, as described above. Based on protein concentrations, samples are diluted to 2mg/ml proteins in ChIP-buffer and 50ul/ml of Protein G Plus-Agarose Suspension Beads (Calbiochem, IP04-1.5ML) are added for 3h to preclear. 2% of the sample is collected as input and kept at -20 °C until DNA purification. Immunoprecipitation is carried out at 4°C overnight with 1ml of sample, 60ul of beads and primary antibody. The beads are then washed once with Wash1, Wash2, Wash3 [0.10% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris (pH 8), 150/200/500mM NaCl for Wash 1,2,3 respectively], Wash LiCl [0.25M LiCl, 1% NP-40, 1% Sodium Deoxycholate, 1mM EDTA, 10mM Tris (pH8)] and twice with TE buffer [10mM Tris (pH8), 1mM EDTA]. Then, beads are resuspended in elution buffer [1% SDS, 0.1M NaHCO3]. The samples are decrosslinked overnight at 65 °C. 20µg of Proteinase K (Sigma, # 39450-01-6) is added for 1h at 42 °C. Then, DNA is purified using BioBasic DNA collection column (BioBasic, #SD5005). DNA concentration was assessed via Picogreen assay (Invitrogen, #P7589). Library were preapred at Genome Quebec (for CTCF and H3K4me3) or The Centre for Applied Genomics (TCAG) at SickKids Hospital (for H3K27ac) using NEB Ultra II DNA kit (no shearing).