Fig. 2

Regeneration-specific genes are activated independent of DNA methylation changes. a Principal component analysis on the transcriptomes of sp7+ and sp7− cells at 0 dpa uninjured fin and 4 dpa blastema. b MA plots for differentially expressed genes during fin regeneration in sp7+ and sp7− cells. Each dot represents log-transformed individual gene expression change. Green and dark gray dots represent statistically significantly upregulated genes during regeneration in sp7+ and sp7− cells, respectively (log₂(FC) > 1 and FDR < 0.05). Blue and black dots represent genes statistically significantly downregulated genes during regeneration in sp7+ and sp7− cells, respectively (log₂(FC) < − 1 and FDR < 0.05). Light gray dots represent genes with no significant changes. c Gene ontology (GO) terms associated with significantly differentially expressed genes. d Examples of expression pattern of upregulated genes during regeneration that fall within the top GO terms. e DNA methylation levels over 10 kb around the promoters and putative distal enhancers of the significantly differentially expressed genes during regeneration