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Fig. 5 | Genome Biology

Fig. 5

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

Fig. 5

DDM1-mediated gene body methylation is associated with augmented gene expression during defense response under sub-optimal priming conditions. A Averaged CG DNA methylation level around genes with GBM-like at gene bodies (GBM) or promoters (pGBM-like). B,C Boxplots of gene expression of DEGs with strongly demethylated GBM-like in ddm1 (GBM-likeddm1) at gene body and promoter (GBMddm1, pGBM-likeddm1). Expression fold change (log2 (ddm1/Col-0)) of all DEGs at each condition was plotted as control. DEG, differentially expressed gene. D CG methylation, histone H1, H2A.Z, and gene expression profiles of genes with GBM-likeddm1 at gene body and promoter (GBMddm1, pGBM-likeddm1) and GBM-likeweak at gene body and promoter (GBMweak, pGBM-likeweak) in Col-0 and ddm1 under the four treatment conditions. GBM-likeddm1; strongly demethylated GBM-like in ddm1, GBM-likeweak; GBM-like that their methylation levels are weakly affected or not affected in ddm1. E Top 4 enriched GO terms among genes with GBMddm1 under BAsubDC condition. F,G Boxplots of gene expression fold change (log2 (BAsubDC/mock)) in Col-0 and ddm1 plants. Genes subtly upregulated (F) and downregulated (G) in Col-0 were grouped and their expression fold change in Col-0 and ddm1 were plotted. unmethylated; unmethylated genes in both Col-0 and ddm1, GBMddm1; genes with strongly demethylated GBM in ddm1 (vs. Col-0, BAsubDC condition), GBMweak; genes with GBM that their methylation levels are weakly affected or not affected in ddm1 (vs. Col-0, BAsubDC condition). B–D, F,G p-values by Student’s t test. n.s.; not significant (p > 0.05)

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