Fig. 3

Candidate regulatory elements for enhancer activity during heart regeneration. (A) Volcano plot of differential ATAC-seq peaks in 3 dpa versus uninjured (Ctrl) samples. The top 20 upregulated peaks with the highest fold changes are marked with the annotated genes. ncam1a, gnai3 and rgmb are in red. N/A, no gene is annotated to the peak. (B) Dot plot of differential ATAC-seq peaks linked to nearby differential transcripts in 3 dpa versus uninjured (Ctrl) samples. Each dot indicates an individual ATAC-seq peak and is counted into the total peak numbers of each quadrant. The number of unique genes in each quadrant is indicated in each corner. The most differential peaks of a few genes are marked with gnai3 and rgmb in red. (C) Heat map of differential transcripts in 3 dpa versus uninjured (Ctrl) linked to nearby differentially accessible chromatin regions. (D) Venn diagram comparison of differentially regulated ATAC-seq peaks in 3 dpa versus uninjured compared with the zCNE list. (E) Enriched motifs in the conserved open chromatin regions with increased (left) or decreased (right) accessibility at 3 dpa. P-value for each enriched TF is shown in the bracket. (F) Browser tracks of the genomic region near gene ncam1a showing the transcripts and chromatin accessibility profiles in the epicardium. The whole-ventricle H3K27Ac profile of the uninjured (Ctrl) and regenerating (Reg) heart is shown at the bottom. zCNE sites are depicted as short black bars. Gray boxes, red arrows and numbers indicate candidate TREEs.