Fig. 3: H2A.Z, H2Aub, and H3K27me3 decrease along with H3K4me2 in atx3/4/5.

a–e ChIP-seq for H3K4me2, H2A.Z, H2Aub, and H3K27me3 in WT and atx3/4/5. a Overlap of genes with decreased H3K4me2 in atx3/4/5 compared to WT (H3K4me2 change (atx3/4/5–WT) < –5) between two biological replicates. The overlapping genes are defined as “ATX3/4/5-target genes (n = 5842)”. b Scatter plots showing the levels of H3K4me2, H2A.Z, H2Aub, and H3K27me3 comparing WT and atx3/4/5. Each dot represents a protein-coding gene. Blue dots indicate ATX3/4/5-target genes (n = 5842). c Box plots showing the changes in H3K4me2, H2A.Z, H2Aub, and H3K27me3 (atx3/4/5–WT) in ATX3/4/5-target genes (n = 5842) and other genes (5842 genes were randomly selected from genes other than ATX3/4/5-target genes). The p-values from two-sided Mann-Whitney U tests are shown. d Metaplots show the averaged distribution of H3K4me2, H2A.Z, H2Aub, and H3K27me3 in WT (black) and atx3/4/5 (blue) in ATX3/4/5-target genes (n = 5842) and all protein-coding genes (n = 27,443). e Box plots showing the relationship between the change in H3K4me2 and the change in H2A.Z, H2Aub, and H3K27me3 in atx3/4/5 compared to WT. Histograms above the boxplots indicate the number of genes in each category of H3K4me2 change. The values of scatter plots, metaplots, and box plots represent RPKM. An additional series of the ChIP-seq analyses for (b and d) showed reproducible results (Supplementary Fig. 3a, b). Box plots in (c and e) display the median (center line), the IQR (box bounds), and the maximum and minimum values within 1.5 IQR (whiskers).