ChIP was conducted as detailed in a previous publication (35, 39). Briefly, 3 g of 10-day-old seedlings was formaldehyde-fixed, and the nuclei were extracted and sonicated. After the chromatin was precleared with protein A or protein G magnetic beads, the protein-DNA complexes were precipitated with anti-HA (H9658, lot: 095M4778V; Sigma-Aldrich), anti-H3K4me2 (07-030, lot: 2840488; Millipore), anti-H3K4me3 (ab8580, lot: GR288375-1; Abcam), anti-H3K27me3 (07-449, lot: 2826067; Millipore), or control IgG serum. The protein-DNA complexes were heated to reverse the cross-linking. The DNA was extracted and amplified by PCR. The gene-specific primers are shown in Data file S1.

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