Fig. 4 | Nature Communications

Fig. 4

From: Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies

Fig. 4

Examples of IBD-upregulated enhancers and linked TSS and genes. Each larger panel shows: genome browser with the average CAGE expression in TPM on both strands, UCSC gene models, TSS-enhancer-linkage through expression correlations (Pearson correlation coefficients are indicated by color, only positive correlations are shown) and CAGE-defined enhancers (black). Green indicates data on forward strand, purple on the reverse strand. Left part of lower panel shows a zoom-in of the enhancer region, with CAGE signal intensity as above, ENCODE DHS peaks and TF ChIP-seq peaks26,66. ChIP-seq peaks are labeled with cognate TF name. Primer locations for qPCR analysis are indicated as double arrows. Right lower panel shows corresponding qPCR analysis of eRNA expression in CDa, UCa and Ctrl samples on both strands as boxplots, relative to the PIAS4 reference gene. a An enhancer upstream of the NOD2 TSS. An enhancer region was detected upstream of the TSS of NOD2, a key gene in IBD pathogenesis with strong support from ENCODE cell line data. b An enhancer in the CXCL1-3,5,6,8 cytokine cluster. Several enhancer regions within a cluster of chemokine genes (CXCL1-3, CXCL5-6, and CXCL8, all upregulated in IBD) were detected. The analysis is focused on a single enhancer linked to the above gene TSSs (for ease of visualization, only links between this enhancer and TSSs are shown). c An enhancer between CXCR1 and CXCR2. An enhancer between CXCR1 and CXCR2 (receptors for the cytokines in panel b) was detected. This enhancer overlapped multiple ENCODE TF ChIP-seq peaks, and the UC-associated rs11676348 SNP. Note the two alternative TSSs for CXCR2. In the lower panel, a track with disease-associated SNPs is shown

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