Analysis of the contributions of PKL, CLF, and PIE1 to gene expression, H2A.Z levels, and H3K27me3 levels in Arabidopsis

ChIP-seq was performed using anti-H3, anti-H3K27me3, and anti-H2A.Z antibodies in three-week-old WT, pkl-1, clf-28, and pie1-5 shoots using paired-end sequencing. Strand-specific RNA-seq was performed on RNA extracted from the same biological samples. RNA-seq analyses used three independent biological replicates. ChIP-seq analyses used two independent biological replicates. Four genetic backgrounds were examined: WT, pkl-1, clf-28, and pie1-5.