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Fig. 8 | Genome Biology

Fig. 8

From: DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis

Fig. 8

Genes with highly variable gene body methylation in the natural population are overlapped with DDM1-mediated gene body methylation. A Scatter plot of the number of natural variants of which methylation status is unmethylated (x-axis) or GBM (y-axis). Each dot represents a gene. The yellow color indicates the highest density, and blue means the low density of genes. GBMNV; genes with stable GBM over 700 natural variants, IMNV; genes with interchangeable GBM (possess GBM at 100–700 natural variants), UMNV; genes unmethylated in over 700 natural variants. Marginal histograms show the distribution for the number of genes. B A boxplot of gene length of gene groups in A. C A violin plot and boxplots of H2A.Z level, responsiveness, and normalized CV2 of gene groups in A. Responsiveness score and normalized CV2 were calculated as Aceituno et al. [69] and Cortijo et al. [60]. D Venn diagram of DDM1-mediated GBM genes (GBMddm1) and genes with interchangeable DNA methylation in the natural population (IMNV) [64, 68]. p-value by Fisher’s exact test. E Top 5 enriched GO terms of gene groups in A. F Relative expression of novel priming regulators in natural variants. (Top) The average GBM level of GPK1 and BRL3 in GBM variants and demethylated variants. (Bottom) Expression of GPK1 or BRL3 under mockDC condition was normalized to 1. Six natural variants and Col-0 were grouped by their GBM level at GPK1 and BRL3. Col-0, Kondara, and UK-1 maintained GBM at both genes, and Ann-1, Bik-1, Kas-1, and Kro-0 lost GBM at GPK1 and BRL3. RT-qPCR data from three replicates per natural variant were averaged (n = 9 for GBM variants, n = 12 for demethylated variants). Yellow color indicates demethylated variants with non-synonymous mutation in each gene (Bik-1, Kro-0 in GPK1; Ann-1, Kas-1 in BRL3). Error bars indicate standard deviation. p-values by Student’s t test

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