Fig. 3: Epigenetic features of rice promoters and associated transcription patterns.

a Comparison of promoter Clusters 1−3 and Cluster 4, defined by epigenetic modification patterns around promoters in Supplementary Fig. 7. b The refinement of promoter regions with H3K4me3 modification and open chromatin signal on transcription activation. A transient reporter assay was used to examine the effects of different promoter regions on gene expression in rice protoplasts. Left, schematic representation of fLUC reporter constructs fused with the full-length promoter (FL) and deletion variants (Δ500, ΔK4me3, FaireK4me3, and ΔFaire). Each value represents the mean ± standard error of mean (n = 3 biological replicates). Empty vector served as the negative control. Gene MH07g0100900 serves as a representative example. c Representative examples for transcription effects of promoter length, open chromatin, and H3K4me3-modified regions on transcription activity, validated by the presence of InDels and PAVs between MH63 and ZS97. Dotted boxes represent the regions with deleted peaks of FAIRE or H3K4me3 in ZS97. d Validation of co-occupation for H3K4me3 and H3K27ac using ChIP-reChIP. Venn diagram (left panel) showing the overlap of H3K4me3 and H3K27ac co-occupation sites dedicated using ChIP-reChIP-Seq and ChIP-Seq, respectively. Boxplots (right panel) for expression levels of the indicated gene category. Boxplots show the median, third and first quartiles. ***p < 0.001 from Wilcoxon test. The numbers indicate the sample size used in the analysis. e Genome browser screenshot showing H3K4me3- and H3K27ac-commodified genes. Source Data underlying Fig. 3b, d are provided as a Source Data file.