Fig. 5: Epigenetic characteristics of open chromatin region and enhancer-like promoter.

a Venn diagram showing the overlap between distal regulatory element (DRE) and proximal regulatory element (PRE) in the mature leaf, panicle, and root of MH63. DREs and PREs were defined in Supplementary Fig. 15. b Epigenetic features of DREs and PREs in mature leaf. Element regions were scaled to equal size. c Heatmap of tissue-specific DREs showing dynamics between the indicated tissues. Tissue-specific DREs were divided into nine clusters based on their signal intensities. d Boxplots of the expression levels of genes proximal to the tissue-specific DRE in the clusters defined in (c). n = 4113, 3067 and 3465 are the number of genes in clusters 1−3, respectively. ***p < 0.001 from Wilcoxon test. e Validation of DRE and PRE-predicted enhancers. Enhancer-like promoter refers to a promoter occupied by PRE. A transient reporter assay was used to examine the effects of these two types of regulatory elements on gene expression in rice protoplasts. One genic fragment (chr2:28,412,151-28,413,151) without epigenetic signal served as negative control. Each value represents the mean ± standard error of mean (n = 4 biological replicates). f A representative example for enhancer-like promoter with chromatin loops. The representative enhancer-like promoter (MH02g0167000, red) was validated in (h). g Expression level of genes in different categories based on H3K4me3-associated chromatin interaction models and PRE-occupancy. The number of different types of genes were labeled. Boxplots in (d) and (g) include a median with quartiles and outliers above the top whisker. ****p < 0.0001 and *p < 0.1 from Wilcoxon test; ns means no significant. The numbers indicate the sample sizes used in the analysis. Source Data underlying Fig. 5c−e, g are provided as a Source Data file.