Prior to chromatin immunoprecipitation, antibodies (5 μl polyclonal or 5 μg monoclonal) were pre-bound to 200 μl Protein G magnetic beads (Invitrogen, #10004D) by overnight incubation in PBS with 5% BSA; beads were washed and resuspended in PBS with 5% BSA. MEF-depleted mESC were fixed at room temperature with 1% formaldehyde (Sigma-Aldrich, # 252549) for 5 min; fixation was stopped by adding glycine (ICN Biomedical, #ICN808822) to 125 mM. Cell membranes were lysed with cold NP-40 buffer (1% NP40, 150 mM NaCl, 50 mM Tris–HCl; pH 8.0) and nuclei collected by centrifugation at 12,000 × g for 1 min at 4 °C. Nuclear pellets were resuspended at a concentration of 2E8 cells/ml in ChIP sonication buffer (1% SDS, 10 mM EDTA, 50 mM Tris–HCl; pH 8.0) supplemented with protease (Thermo Scientific, #78430) and phosphatase (Calbiochem, #524627) inhibitor cocktails. Chromatin was sheared into 150-400 bp fragments by sonication (Bioruptor Twin, Diagenode). Debris was pelleted by centrifugation and cleared chromatin was diluted 10-fold in ChIP dilution buffer (1.1% Triton X-100, 0.01% SDS, 167 mM NaCl, 1.2 mM EDTA, 16.7 mM Tris–HCl; pH 8.1). The prepared antibody-bound beads were added to 1 ml diluted chromatin containing 2E7 million cell equivalents and incubated overnight with rotation at 4 °C. Immune complexes were washed 5 times with LiCl wash buffer (250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 100 mM Tris-HCl; pH 7.5) and once with TE (0.1 mM EDTA, 10 mM Tris-HCl; 7.5). Beads were resuspended in IP Elution Buffer (1% SDS, 0.1 M NaHCO3) and crosslinks reversed by overnight incubation at 65 °C. DNA was purified by column purification (QIAGEN, # 28106) Sequencing libraries were constructed from DNA samples with the Illumina TruSeq V3 library construction protocol.