Genome-wide H3K4me3 analysis in Arabidopsis

To explore the bivalent histone modifications in the Arabidopsis genome, we examined genome-wide histone 3 lysine-27 trimethylation (H3K27me3) and histone 3 lysine-4 trimethylation (H3K4me3) in 5-day-old seedlings (Col-0) by ChIP-seq. We found that more than 1300 genes loci contain both H3K27me3 and H3K4me3. Nuclei were extracted from 5-day-old WT (Col-0) seedlings as previously described (Louwers et al., 2009), followed by chromatin immunoprecipitation with Magna ChIP A/G kit (Millipore). DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), and subsequently were sequenced on X Ten (Illumina). Three biologically independent samples have been analyzed.