Genome-wide transcriptome and epigenome data analysis of kaku4-2 mutant and WT plants

We conducted ChIP-seq technology to generate epigenomic profiles of H3K4me3, H3K27me3 and H3K9me2 in Arabidopsis leaves for the mutant (kaku4-2) and wild-type (WT) plants. The results showed that knockdown of KAKU4 has the strongest effect on H3K27me3, followed by H3K9me2, and the least effect on H3K4me3, leading to significant change of chromatin states in Arabidopsis genome. KAKU4 may affect the switch between active and repressive chromatin states, especially knockdown of KAKU4 caused the transition between H3K9me2 and H3K27me3 in some specific PLAD regions. The combination analysis of epigenomic and transcriptomic data between kaku4-2 mutant and WT suggested that KAKU4 may regulate some key biological processes, especially programmed cell death and hormone signaling pathways. The ChIP-seq analyses of H3K4me3, H3K27me3 and H3K9me2 were conducted using the 4th-week rosette leaves of kaku4-2 mutant and WT. Rosette leaves of the 30-day-old kaku4-2 mutant and WT plants were sampled for RNA-seq with three independent biological replicates.