Chromatin Immunoprecipitation (ChIP) assays were performed using 1 g 12-day-old seedlings as previously described with minor modifications (Lu F. et al., 2010, Cell research 20(3):387-390). For anti-HA ChIP, chromatin was fragmented by Micrococcal nuclease (MNase, NEB M0247S) in the MNase digestion buffer (50 mM Tris pH 8.0, 0.32 M sucrose, 4 mM MgCl2, 1 mM CaCl2) instead of sonication before nuclei lysis. Antibodies used in ChIP were anti-H3K4me3 (Millipore 07-473) and anti-HA (Sigma H6908). The ChIP-Seq libraries were constructed using NEBNext® DNA Library Prep Master Mix Set for Illumina® (NEB, E6040S). ChIPed DNA was ligated with Illumina single-end genome sequencing adaptors, size fractionated to obtain 300-bp fragments
GEO Accession
GSM1464766