Fig. 3

Combined enrichment of H3K9Ac, H3K14Ac, and H3K23Ac is correlated with high gene expression levels in the presence of ethylene. a Overlap of genes marked by H3K9Ac, H3K14Ac and H3K23Ac under ethylene treatment. b Boxplot showing the association of transcript levels of gene expression and histone acetylation in Col-0 with ethylene treatment Gene expression levels were Log2-transformed. “All genes” indicates the total genes in Arabidopsis; K9 K14 K23, genes marked by H3K9Ac, H3K14Ac and H3K23Ac, n = 9120; K14 K23, genes marked by H3K14Ac and H3K23Ac but not H3K9Ac, n = 343; K14 K9, genes marked by H3K14Ac and H3K9Ac but not H3K23Ac, n = 1909; K23 K9, genes marked by H3K23Ac and H3K9Ac but not H3K14Ac, n = 1339; K14, K23, and K9, genes uniquely marked by K14 (n = 799), K23 (n = 358), or K9 (n = 3455); none, genes that could not be assigned to peaks of H3K9Ac, H3K14Ac, or H3K23Ac. The ** indicates P < 6.04 × 10⁻⁶ by t-test. c Boxplot showing peak breadths under ethylene treatment plotted based on transcript abundance. Genes were ranked according to relative mRNA expression levels and divided into five equal sets. The ** indicates P < 0.001 by t-test. d-f Scatter plots of mean histone enrichment of d H3K9Ac, e H3K14Ac, and f H3K23Ac in ethylene treatment vs. air. To generate the graph, histone reads density were normalized using MAnorm [37] and normalized peak enrichments in ethylene vs. air were plotted for sets of genes clustered based on transcript abundance in air. Solid black lines in the plots denote the linear regression line. g-i Volcano plots for g H3K9Ac, h H3K14Ac, and i H3K23Ac showing the differential enrichment (Rescaled M value versus Rescaled A value after MAnorm normalization [37]) for each individual peak detected in the comparison of plants grown in ethylene vs. air. M = log2 (Read density in C₂H₄/Read density in air) and A = 0.5 × log2 (Read density in C₂H₄ × Read density in air). Red dots represent data with P ≤ 0.05 and |M| ≥0.4