Extended Data Fig. 8: RdDM-dependent regulation of ATREP2 TEs and JA-induced DMRs.
From: Long-lasting memory of jasmonic acid-dependent immunity requires DNA demethylation and ARGONAUTE1
a, Numbers of TEs from the ATREP2, ATREP7 and TNAT1A families overlapping with previously characterised Type I and Type II RdDM targets23 (Type I, RdDM is dominant; Type II, ROS1 is dominant). b, Numbers of JA-induced DMRs (all-C and CHH contexts for all three comparisons; see Fig. 5) overlapping with previously characterised Type I and Type II RdDM targets23. c,d,e,f,g,h, Global DNA methylation patterns by whole-genome bisulphite sequencing of shoot tissues from naïve WT (Col-0), nrpe1-11 and ros1-4. c, PCA displaying variation in global DNA methylation at all-C sequence context between the 4 biological replicates of each genotype. d,e,f, Average % DNA methylation at TEs from the ATREP2, ATREP7 and TNAT1A families in CG (d), CHG (e) and CHH (f) contexts. g,h, Average % DNA methylation at JA-induced DMRs in all-C (g) or CHH contexts (h). For each analysis, n indicates the number of members of each TE family (d,e,f) or DMRs of each comparison (g,h) with sufficient coverage across all three genotypes to be included in the analysis (≥ 5 reads for ≥ 50 % of cytosines).
