Fig. 2: Pathogen infection alters chromatin architecture and gene expression at the EFR and XI-k locus.

a, Cytosine methylation in the CG, CHG and CG contexts at Ea-IR (demarcated by vertical black lines) and flanking regions (700 bp) in Col-0, dcl234 and ddc mutants in mock-treated plants and 1 day after infection with Pst DC3000 hrcC. The average of three individual BS-seq replicates are plotted for each genotype. b,c, Relative expression of EFR, Xl-k and PR1 in Col-0 wild-type (b), and dcl234, ddc and eair-1 (c) plants infected with Pst DC3000 hrcC as measured by RT–qPCR and normalized against ACT2. Samples were collected at different time points after infection (days or hours after infection). RNA levels are expressed relative to the mock-treated (b) or infected (c) Col-0 plants. Values are from n = 3 biologically independent samples. HAI, hours after infection; DAI, days after infection. d,e, Quantification of the formation of Loop^EFR and Loop^Xl-k as measured by 3C–qPCR analysis in Col-0 wild-type, eair-1, ddc and dcl234 plants mock-treated or infected for 1 day with Pst DC3000 hrcC. Values of n = 4 (d) or n = 3 (e) biologically independent samples are expressed relative to the mock-treated samples. In all plots, data are presented as the mean values ± s.d. P values were calculated with a two-tailed unpaired t-test with Welch’s correction.

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