Fig. 3

Regeneration-specific gene activation with gain of chromatin accessibility. a Expression fold changes for the genes with differentially accessible promoters during regeneration. b Epigenome browser views of genes whose activation is concordant with gain of chromatin accessibility of the promoter region (col1a1a, hoxc13a, and lef1). Red dashed boxes highlight ATAC peaks with increasing signals during regeneration. c ATAC-seq signals (left) and DNA methylation levels (right) over 10-kb regions centered on DARs with increasing signals in sp7+ (top heatmap) and sp7− cells (bottom heatmap) during regeneration. Average ATAC-seq signals and DNA methylation levels were plotted on top of each heatmap (line plots). d Identified candidates of regeneration-related enhancers and in vivo validations. Epigenome browser views of regeneration enhancers (top) and transgenic zebrafish carrying candidate sequence-driven reporter showing enhancer activities in the regenerating fin (bottom). Red dashed boxes indicate DARs that gained accessibility during regeneration. Asterisks indicate that F₁ transgenic zebrafish line was established for a given enhancer element