Fig. 4

The alkbh1 mutation increased genome-wide H3K27me3. a Histone H3K4me3, H3K9me2, and H3K27me3 levels in alkbh1 compared to wild types (WT) were detected by immunoblotting. H3 was tested as a loading control. Original images are shown in Additional file 8. b Scatterplots of H3K27me3 ChIP-seq peaks in WT and alkbh1. Total peaks are merged from all samples (n = 11,473). The x-axis and y-axis represent the normalized read number at each peak of WT and alkbh1, respectively. Blue dots represent the downregulated peaks; red dots represent the upregulated peaks; differential H3K27me3 peaks (fold change > 1.5, P < 0.05) overlapping between two replicates were considered as significantly changed. c Heatmaps and metaplots of ALKBH1-binding signals in the genes that showed increased H3K27me3 in alkbh1 (n = 1058), of which 225 showed ALKBH1 binding, and the remaining (833 gray) are unbound genes. d Metaplots of elevated levels of H3K27me3 for ALKBH1-binding and non-binding genes in alkbh1 versus WT. e Boxplots of the expression levels of the two gene categories in c in the wild-type, mutant, and OE plants. The y-axis represents the gene expression level in log2 (TPM + 0.01). The center line stands for the median, box limits stand for the upper and lower quartiles, and whiskers stand for 1.5 × the interquartile range. The dotted line is TPM equal to 1. Statistical significance between comparisons was calculated by Student’s t-test. *P < 0.05, **P < 0.01, ***P < 0.001. ns, no significant difference. f Heatmaps and metaplots of ALKBH1 binding and chromatin modifications signals in the genes that showed increased H3K27me3 in alkbh1 (n = 1058). The top 225 genes are ALKBH1-binding genes