Fig. 3

Gene-associated ChIP-Seq peaks in each condition of interest. A Workflow of peak enrichment from conditions of interest compared to untreated WT to identify unique or 2-fold enriched peaks before progressing with further analysis. B Venn diagrams showing number of genes differentially acetylated (H4ac) or methylated (H3K27me3) associated with conditions of interest (WT +MeJA, axe1-5 and axe1-5 +MeJA). Genes were determined to be differentially acetylated/methylated with respect to the untreated WT if the enrichment of the corresponding peak summit was at least ≥ 2 fold or where a peak associated with that gene was absent altogether in the untreated WT. axe1-5 +MeJA showed the greatest proportion of enriched genes: 69.82% (2709/3880) and 63.16% (696/1102) of the total for H4ac- and H3K27me3 respectively. The lowest proportion was associated with axe1-5: 31.03% (1204/3880) and 15.88% (175/1102) of the total for H4ac- and H3K27me3 respectively. Diagrams created in BioVenn [73]. C Heatmap and dendrogram showing hierarchical clustering of enrichment of genes associated with H4ac (red) and H3K27me3 (blue) in the three conditions. Clustering was performed using k-means clustering of Euclidean distances of differential enrichment values associated with each gene with respect to the untreated WT. Values were subsequently scaled by row to generate Z-scores of enrichment (see scale bar)