Skip to main content
. 2022 Apr 11;13:1945. doi: 10.1038/s41467-022-29551-7

Fig. 2. ChIP-seq and ATAC-seq data accurately predict functional pancreatic enhancers.

Fig. 2

a Average expression of genes interacting with putative pancreas-specific enhancer sequences (PsE), detected by HiChIP for H3K4me3 (HC, n = 6174 genes), compared to the average expression of all genes (AllG, n = 33737 genes). Gene expression was determined from RNA-seq data from different pancreatic cells (acinar n = 4, duct n = 3, endocrine pancreas n = 4), whole pancreas (n = 2), and muscle (control; n = 2). One-sided Wilcoxon test (≥), p-values < 0.05 were considered statistically significant (****p < 2E−16). Error bars represent the 95% confidence interval. b Ratio between average expression of genes interacting with putative pancreatic enhancers (PsE, C1, C2, C3 and C4 clusters) and the average expression of all genes throughout zebrafish development. C1, C2, C3 and C4 are different clusters that compose the DevE category. BDO: blastula, dome; G50: gastrula, 50% epiboly; GSH: gastrula, shield; G75: gastrula, 75% epiboly, S1–4: segmentation, 1–4 somites; S14–19: segmentation, 14–19 somites; S20–25: segmentation, 20–25 somites; PP5: pharyngula, Prim-5; PP15: pharyngula, Prim-15; PP25: pharyngula, Prim-25; HLP: hatching, long-pec; LPM: larval, protruding-mouth; LD4: larval, day 4; LD5: larval, day 5. c Percentage of F0 zebrafish larvae with GFP expression in the exocrine pancreas following in vivo transient transgenesis reporter assays. The empty enhancer reporter vector was used as the negative control (NC). The depicted sequences (E1 to 10) represent the top 10 putative enhancer sequences with higher H3K27ac signal (“high H3K27ac” group). Values are represented as percentages and compared by two-sided Chi-square with Yates’ correction test. p-values<0.05 were considered significant (****p < 0.0001, *p < 0.05). The exact p-value and n are discriminated in Supplementary Dataset 4. d Representative confocal image of the in vivo transient transgenesis reporter assays for the E3 sequence (n = 30). depicted in c) showing expression of GFP (green) in 11 dpf zebrafish pancreas (white dashed line), labelled by anti-Alcam staining (white) and anti-Amylase (red) antibodies (n = 30, from 2 independent injections, with 63.33% of larvae showing GFP expression in the exocrine pancreas). Nuclei were stained with DAPI (blue). Images were captured with a Leica SP5II confocal microscope. Scale bar: 60 µm. For a–c, source data are provided as a Source Data file.