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. 2020 Jul 7;11:3383. doi: 10.1038/s41467-020-17205-5

Fig. 2. Enhancer—gene annotation.

Fig. 2

a The volcano plot illustrates the 919 down- (blue) and 1716 upregulated genes (green) using RNA-seq data. b GREAT was used to annotate enhancers to genes. The pie plot shows how many genes were annotated to enhancer elements. c The pie plot illustrates the distance between the enhancers and their annotated genes (in kb to the transcriptional start site (TSS)). d 571 enhancer elements are annotated to the 919 downregulated genes (62%, dark blue). 1076 enhancers are assigned to 1716 upregulated genes (63%, dark green). e Genes associated with IRI-decreased enhancers (n = 6512) are significantly downregulated, whereas genes assigned to IRI-increased enhancers (n = 9774) have a significantly higher gene expression compared to genes assigned to SHARED enhancers (n = 16781). Median, middle line inside each box; IQR (interquartile range), the box containing 50% of the data; whiskers, 1.5 times the IQR. One-way ANOVA with Tukey post hoc test was applied. f Slc34a1 and Kl are representative genes that were down-regulated in IRI day 2 when compared with SHAM. Havcr1(encoding KIM-1) is a gene significantly upregulated at IRI day 2. Two-sample t-test was applied (two-sided). Individual data points and box-plot with mean ± max, min are shown. n = 4 biologically independent samples g Illustration of the enhancer landscape of Slc34a1. The indicated enhancers show a lower coverage of H3K27ac, and a strongly reduced coverage of BRD4 and Pol II with IRI compared to SHAM. The coverage of BRD4, Pol II and H3K4me3 is also strongly reduced over the promoter with IRI. RNA-seq track shows reduced expression on exon elements after injury. h Depiction of the enhancers associated to Kl. These enhancers show a strong decrease of H3K27ac, BRD4, and Pol II. In addition the promoter loses H3K27ac, BRD4, Pol II, and H3K4me3 binding. RNA-seq track shows reduced expression on exon elements after injury. i Havcr1 gains an enhancer element at IRI day 2. Also the promoter shows an increased coverage of H3K27ac, BRD4, Pol II, and H3K4me3. RNA-seq track shows increased expression on exon elements after injury.