Fig. 4

DDM1-mediated transposon-like methylation (TEM-like) at transcription start sites (TSS) and gene bodies is associated with augmented gene expression during defense response under sub-optimal priming conditions (BAsubDC). A Averaged CG DNA methylation level around genes with TEM-like at TSS, gene bodies, or promoters. B–D Boxplots of gene expression of DEGs with strongly demethylated TEM-like in ddm1 (TEM-like^ddm1) at TSS, gene body, and promoter (TSS TEM-like^ddm1, gbTEM-like^ddm1, pTEM-like^ddm1). Expression fold change (log₂ (ddm1/Col-0)) of all DEGs at each condition was plotted as control. DEG, differentially expressed gene. E CG, CHG, CHH methylation, histone H1, H2A.Z, and gene expression profiles of genes with TEM-like^ddm1 at TSS, gene body, and promoter (TSS TEM-like^ddm1, gbTEM-like^ddm1, pTEM-like^ddm1) and TEM-like^weak at TSS, gene body, and promoter (TSS TEM-like^weak, gbTEM-like^weak, pTEM-like^weak) in Col-0 and ddm1 under the four treatment conditions. TEM-like^ddm1; strongly demethylated TEM-like in ddm1, TEM-like^weak; TEM-like that their methylation levels are weakly affected or not affected in ddm1. B–E p-values by Student’s t test