The MNase assays were carried out as described previously (50 (link)) with minor modifications. Approximately 400 milligrams of seedlings were used per sample. Additionally, equal amounts of spike-in nuclei extracted from Saccharomyces cerevisiae were added to each sample before MNase treatment, which worked as the internal control among samples (51 (link)). For MNase treatment, the prepared nuclei were resuspended in prewarmed MNase digestion buffer, followed by the addition of 8 units of MNase (Cat. 2910A, TaKaRa) and incubation (15 min at 37°C with periodic agitation). Finally, the mono-nucleosomal DNA was isolated from 2% agarose gels and quantified by the Qubit dsDNA HS assay kit (Cat. Q32851, ThermoFisher SCIENTIFIC).
For MNase-qPCR, the nucleosome occupancy for a specific region was determined as the percentage of input-MNase-digested DNA, which was then normalized to the spike-in-control yeast NUC6. Primers used for qPCR are listed inSupplementary Dataset S1 . The locations of primers on each gene used for qPCR are shown in Supplementary Figure S1 . For MNase-seq, DNA libraries were generated following the published protocol (42 (link)).
For MNase-qPCR, the nucleosome occupancy for a specific region was determined as the percentage of input-MNase-digested DNA, which was then normalized to the spike-in-control yeast NUC6. Primers used for qPCR are listed in
