Fig. 4

Association between chromatin compactness, DNA methylation, and gene expression. a Distribution of A. thaliana chromatin compactness ratios between the hybrid and parent, calculated in 5-kb bins. Areas highlighted in yellow and magenta indicate the bottom and top 10% bins, respectively. b DNA methylation of bins highlighted in (a). c Distribution of gene expression ratios between hybrid and A. thaliana parent in regions highlighted in (a). Every gene is assigned to a 5-kb bin based on its TSS. Bkg background consisting of all genes. All comparisons have p values > 0.05 from Wilcoxon–Mann–Whitney tests. d, e Relationship between chromatin compactness and differentially expressed genes. Bins of 5 kb are colored red (d) or green (e) if there is at least one upregulated or downregulated gene located in them. For both panels, all pairs of comparisons have p values > 0.05 from Wilcoxon–Mann–Whitney tests