Fig. 2

Fig. 2 Endothelium-specific inhibition of Brg1 changes the levels of H3K4me3 in the promoter regions of the zebrafish genome.

a Heatmap displaying Z-score normalized gene expression for differentially expressed genes between FACS-sorted kdrl:EGFP endothelial cells from dominant-negative Brg1 groups (DNK1 and DNK2) and control groups (CtrlK1 and CtrlK2). FPKM value of each gene was normalized using Z-scores across samples. Columns represent individual samples (two biological replicates for each group); rows represent differentially expressed genes ordered by hierarchical clustering. Labeled genes are part of the differentially expressed Notch signaling genes. The upregulated genes in the DNK group that were labeled with ‘red color’ had H3K4me3 peaks in their promoters. b Venn plot representing the intersection of H3K4me3 peaks between Ctrl and DN groups. c Heatmaps and summary plots displaying the signal profile of normalized read coverage around three categories of H3K4me3 peaks across different samples. The read coverage was normalized to 1x sequencing depth in all samples. Each row of the heatmap represents one peak, with coverage plotted across the 3 kb surrounding the peak summit. H3K4me3 peaks were classified into three categories: Ctrl-Specific Peaks represent peaks specifically in the Ctrl group; Overlapped Peaks represent peaks overlapped between the Ctrl and DN groups; DN-Specific Peaks represent peaks specifically in the DN group. The genomic distribution for three types of peaks is presented with pie charts on the right side. d Venn plot representing the intersection between genes with promoters marked by Overlapped Peaks and DN-Specific Peaks and genes that were differentially upregulated in the DNK group.