E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 15% ES FBS (Gibco), 2mM L-glutamine (Gibco), 1X PenStrep (Gibco), 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco), 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore)),  3 μM CHIR99021 (Tocris) and 1 μM PD0325901 (Tocris). NrESC medium is composed of ESC medium supplemented with 10 µM T0901317. All the ESC lines used in this study were cultured on gelatin-coated tissue culture plates and all the cell lines were cultured at 37°C with 5% CO 2 . Cells were trypsinized, harvested and the cell number was estimated. Cross-linking was performed for 10 × 106 cells using 1% formaldehyde for 10 min at room temperature followed by quenching with 0.125 M Glycine. Crosslinked cells were resuspended in 1 ml of FA lysis buffer (10 mM Tris–Cl (pH 8), 100 mM NaCl, 10 mM EDTA, 0.25% Triton X-100 and protease inhibitor cocktail (Roche)), nutated at 4 °C for 15 min and spun down at 1300 × g for 5 min at 4 °C. Supernatant was removed and the pellet was re-suspended in 1% SDS lysis buffer (50 mM HEPES–KOH (pH 7.5), 150 mM NaCl, 1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC and protease inhibitor cocktail). After 15 min of incubation, the pellet was spun down and washed two times with 0.1% lysis buffer (50 mM HEPES–KOH (pH 7.5), 150 mM NaCl, 0.1% SDS, 2 mM EDTA, 1% Triton X-1s00, 0.1% NaDOC and protease inhibitor cocktail). Cell pellet was sonicated by Biorupter (Diagenode) for 14 cycles (30 s on and 60 s off for each cycle). Cell debris was removed from the sheared chromatin by centrifugation at 21,000 × g at 4 °C for 30 min. Protein G Dynabeads (Life Technologies) was incubated with antibodies (Nr1h2 ChIP antibody (NB100-1464, Novus Biologicals), FLAG ChIP antibody (F1804, Sigma-Aldrich), H3K9me2 ChIP antibody (Abcam, ab1220), H3K9me3 ChIP antibody (Abcam, ab8898) and H3K27Ac ChIP antibody (ab4729, Abcam)) for 3 h at room temperature and washed three times by PBS with 0.1% TritonX-100. 5% of the sheared chromatin was separated as input while the remaining was subject to overnight incubation with antibody-bound Dynabeads. In total 7 washes were performed to remove unspecific bindings, including three washes with 0.1% SDS lysis buffer, one with 0.1% SDS lysis buffer/0.35 M NaCl, one with 10 mM Tris–Cl (pH 8.0), 1 mM EDTA, 0.5% NP40, 0.25 LiCl, 0.5% NaDOC, and two with TE buffer (pH 8.0). Dynabeads were resuspended in elution buffer (50 mM Tris–HCl (pH 7.5), 10 mM EDTA, 1% SDS) and incubated at 68 °C for 1 h with 1400 rpm shaking. Eluted samples were de-crosslinked at 42 °C for 2 h and 67 °C for 6 h with Pronase (Sigma). DNA purification was further performed with QIAGEN PCR Purification kit (for inputs) and the QIAGEN MinELute PCR Purification kit (for ChIP samples). Quantitative PCR with CXF384 Real-time System (Bio-Rad) and Kapa SYBR Fast qPCR kit (Kapa Biosystems). For ChIP-seq library preparation, ACCEL-NGS®2S Plus DNA library kit (IDT) and 2S™ Adapter Set A (IDT) was used as per manufacturer's instruction starting with 5–10 ng DNA for both input and ChIP sample.