Fig. 2

Genome-wide analysis of H3K9Ac, H3K14Ac and H3K23Ac in etiolated seedlings in the absence of ethylene. a Overlap of peak-associated genes among H3K9Ac, H3K14Ac and H3K23Ac in Col-0 under air treatment. The nearest gene was assigned to each peak if there was more than one gene within 5 kb. b The correlation of histone enrichment (RPKM) of H3K14Ac vs. H3K23Ac; H3K14Ac vs. H3K9Ac; and H3K23Ac vs. H3K9Ac in gene body regions with transcript abundance in the absence of ethylene. “All genes” indicates the total genes in Arabidopsis. Genes were ranked according to relative mRNA expression levels and divided into five equal sets. c Boxplot showing the association of transcript levels of gene expression and histone acetylation in Col-0 without ethylene treatment. Gene expression level was Log2-transformed. “All genes” indicates the total genes in Arabidopsis; K9 K14 K23, genes marked by H3K9Ac, H3K14Ac and H3K23Ac, n = 2400; K14 K23, genes specifically marked by H3K14Ac and H3K23Ac but not H3K9Ac, n = 172; K14 K9, genes specifically marked by H3K14Ac and H3K9Ac but not H3K23Ac, n = 202; K23 K9, genes specifically labeled by H3K23Ac and H3K9Ac but not H3K14Ac, n = 1529; K14, K23, and K9, peak associated genes uniquely marked by K14 (n = 25), K23 (n = 513), and K9 (n = 5927), respectively; none indicates genes not associated with H3K9Ac, H3K14Ac, or H3K23Ac peaks. The ** indicates P = 5.49 × 10⁻¹¹ by t-test. d-f Boxplots showing the correlation of peak breadths for H3K9Ac (d), H3K14Ac (e), and H3K23Ac (f) with gene expression levels in genome wide. Genes were ranked according to relative mRNA expression levels and divided into five equal sets. The ** indicates P ≤ 3.25 × 10⁻¹⁸ by t-test. No significant differences within gene groups were detected between H3K14Ac and H3K23Ac gene sets (P value >0.01)