Chromatin immunoprecipitation (ChIP) assays were performed as previously described with modifications.55 Briefly, 4 g of 2-week-old seedlings were frozen in liquid nitrogen and ground to a fine powder, followed by cross-linking in 50 mL of nuclei isolation buffer I (0.4 M sucrose, 10 mM HEPES pH 7.5, 10 mM MgCl2, 5 mM β-mercaptoethanol, 0.1 mM PMSF, and 1× protease inhibitor cocktail) containing 1% (v/v) formaldehyde for 10 min at room temperature. The reaction was quenched with 3.4 ml of 2 M glycine. Chromatin was extracted by filtering through two layers of Miracloth and pelleted by centrifugation. Nuclei were subsequently isolated using NIB buffer (20 mM Tris-HCl pH 7.5, 25% [v/v] glycerol, 0.25 M sucrose, 2.5 mM MgCl2, 10 mM NaCl, 0.5% [v/v] Triton X-100, 0.5 mM spermidine, 0.15 mM spermine, 10 mM β-mercaptoethanol, 1 mM PMSF, and protease inhibitors) and lysed in nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% [w/v] SDS, 1 mM PMSF, and protease inhibitors) for 30 min on ice. Chromatin was sheared to fragments using a Bioruptor sonicator (Diagenode) with 18 cycles of 30 sec ON/30 sec OFF. Immunoprecipitation was performed using anti-FLAG antibody (Sigma, H7425) conjugated to a 1:1 mixture of Protein A/G magnetic beads (Sigma, 16-663) in ChIP buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and protease inhibitors). Beads were sequentially washed with low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100), high salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 0.1% SDS, 1% Triton X-100), LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% sodium deoxycholate, 1% NP-40), and TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Immunoprecipitated DNA was eluted in 100 μL elution buffer (1% SDS, 0.1 M NaHCO3) at 65°C for 15 min, followed by proteinase K digestion (20 μg/mL) in the presence of 0.5 M EDTA and 20 mM Tris-HCl (pH 6.5). Purified DNA libraries were sequenced on an Illumina HiSeq 2100 platform (Novogene) with 150 bp paired-end reads.