Fig. 3

ALKBH1 genome-wide binding characteristics. a Metaplots and heatmaps of ALKBH1-binding signals (centered in the binding peaks) in the wild type and alkbh1#1 mutant. b Metaplots and heatmaps of H3K27me3 and H3K4me3 levels in ALKBH1-binding genes. c Scatterplots of the differentially expressed genes in alkbh1 with the ALKBH1-binding genes. The x-axis and y-axis respectively represent the normalized reads number of the DEGs (log₂FC > 1, q-value < 0.05) in alkbh1 and in the wild type. The blue dots represent the ALKBH1-binding genes. P-values were calculated by hypergeometric tests. d Scatterplots of the DEGs in OEALKBH1 with the ALKBH1-binding genes. The x-axis and y-axis respectively represent the normalized reads number of the DEGs (log₂FC > 1, q-value < 0.05) in OEALKBH1 and in the wild type. The red dots represent the ALKBH1-binding genes. P-values were calculated by hypergeometric tests. e Metaplots and heatmaps of chromatin modification profiles in the ALKBH1-binding genes that are downregulated in alkbh1 (n = 324 blue), upregulated in OEALKBH1 (n = 349 red), and unchanged in the mutant or OE plants (n = 1133 gray). f Boxplots of H3K4me3/H3K27me3 ratios of the ALKBH1-binding genes that are downregulated in the mutant (324), upregulated in OE plants (349), and unchanged in the transgenic plants (1133). Statistical significance between wild type and alkbh1 was calculated by Student’s t-test. *P < 0.05, **P < 0.01, ***P < 0.001. ns, no significant difference