Fig. 4

Differences in IRE-gene regulatory landscapes affect transcriptional responses upon injury. A-C Upper, boxplots showing expression level changes of common (A), zebrafish-specific (B), or mouse-specific (C) IRE-associated genes (orange) compared to the other genes (used as background) (blue) in zebrafish and mice. P-values: Wilcoxon rank-sum test. Middle, metagene plots displaying smoothed H3K27ac ChIP-seq signals (zebrafish: normalized read counts, mouse: log2 transformed read counts over corresponding input samples) at the regions around TSSs (from -5 kb to + 5 kb) of common (A), zebrafish-specific (B), or mouse-specific (C) genes in zebrafish and mice (orange: uninjured, blue: regenerating). Bottom, heatmaps showing H3K27ac ChIP-seq signals around TSSs (from -5 kb to + 5 kb) of common (A), zebrafish-specific (B), or mouse-specific (C) genes upon injury in zebrafish and mice. Each row represents a single gene. Red stands for high density, and white or blue for low signal. D-I Upper, boxplots displaying expression level changes of a representative common (D, “cell activation”; E, “TNF signaling pathway”), zebrafish-specific (F, “dendritic cell differentiation”; G, “parathyroid hormone synthesis, secretion and action”), or mouse-specific (H, “cell–cell adhesion”; I, “adherens junction”) GO term or KEGG pathway associated genes (orange) compared to the other genes (as background) (blue) upon cardiac injury. P-values: Wilcoxon rank-sum test. Middle and lower, metagene plots (middle) or heatmaps (lower) showing H3K27ac signals at the regions around TSSs (from -5 kb to + 5 kb) of common (A), zebrafish-specific (B), or mouse-specific (C) genes in zebrafish and mice. The meaning of labels is the same as (A-C)