Cells were trypsinized and chemically cross-linked with 1% methanol-free formaldehyde (Cat#04018, Polysciences) for 10 min at room temperature, then quenched with 0.125 M glycine. Fixed cells were lysed sequentially in lysis buffer I (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 0.25% Triton X-100, 0.5% NP-40, 10% glycerol, 1 mM EDTA), lysis buffer II (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), followed by lysis buffer III (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine). Chromatin fractions were sheared to 200–500 bp using Bioruptor® Plus sonicator under high power setting for 20 cycles (30 seconds ON, 30 seconds OFF). The sheared DNA was measured on an Agilent 2100 Bioanalyzer using High Sensitivity DNA Analysis Kits (Agilent, Cat#5067-4626). The high-size fragments (> 500 bp), if detected, was then removed with size-selection using Agencourt AMPure XP beads (Cat#A63881, Beckman Coulter). The sheared DNA then was incubated using appropriate antibodies (and the same amount of control IgG for ChIP-qPCR) overnight and then precipitated with Protein G Dynabeads (Cat#10004D, Thermo Scientific). Precipitates were washed sequentially using the following washes for 5 minutes each: low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), high salt buffer (20 mM Tris-HCl pH 8.0, 500mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), 1X LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% deoxycholate, 1% NP-40) and twice in 1X TE buffer + 50 mM NaCl. Chromatin-antibody-beads were eluted in 50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS and de-cross-linked in 5 M NaCl solution at 65°C overnight. Sheared DNA was purified using the Zymo ChIP DNA Clean & Concentrator kit (Cat#D5201, Zymo) for ChIP–seq library preparation. ChIP-seq libraries were prepared using the NEBNext Ultra DNA Library Prep kit for Illumina according to manufacturer's instructions.