Fig. 2 | Nature Communications

Fig. 2

From: Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation

Fig. 2

Characterization of H3K4me3-associated promoter–promoter interactions. a Global view of H3K4me3-associated interactions and epigenetic and transcriptional features on chr4. Zoomed-in view of detailed loop and peak distributions at the indicated regions. b Chromatin models. The BP model, genes with binding sites that are not involved in chromatin interactions. The PPI model, genes with anchor sites involved in interactions. P promoter; solid curve, chromatin loop. c Pie chart for the percentage and number of genes engaged in H3K4me3-associated chromatin models. d Boxplot for intensities of H3K4me3 peaks (left) and expression levels of BP and anchor genes (right). ***p < 0.001 from Wilcoxon test. e Expression breadth of H3K4me3 anchor and BP genes. Random genes served as control. p < 2.2e−16 from Kruskal–Wallis test. f Distribution of core and distributed genes that participated in PPI models. Core genes, present in more than 99% of 453 rice accessions; distributed genes, present in <99% of 453 rice accessions. g Contour plot of log-transformed FPKM values for H3K4me3 anchor gene pairs. h Histogram for co-expression analysis of H3K4me3 anchor gene pairs. The mean PCC of anchor gene pairs is much higher than that of both (A) randomly simulated gene pairs and (B) randomly selected H3K4me3-marked gene pairs which have the same physical distance with anchor gene pairs. i H3K4me3-associated PPI network from chromosome 3. The size of the circles is proportional to the degree (connection frequency) of the genes (as nodes). The redder color indicates higher gene expression. j A screenshot of a H3K4me3-associated cluster in dotted line box area of h. k Boxplot shows the positive relationship of the degrees of genes with transcriptional activity. Gene numbers in each category are given. l Co-expression analysis of genes in H3K4me3-associated subnetworks. The PCC of subnetworks are calculated. Random, randomly selected gene pairs. Actual, all H3K4me3 anchor gene pairs. ***p < 0.001 from Wilcoxon test. Boxplots in d, k, l show the median, and third and first quartiles. Source data of d, k are provided as a Source data file

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