Early epigenetic priming of regeneration studied with a novel transgenic epigenetic reporter

Abstract

Tissue regeneration requires previously differentiated cells to regain developmental plasticity. However, the upstream mechanisms initiating this process remain poorly understood. Here, we leverage a novel "EpiTag" transgenic zebrafish reporter line that enables real-time visualization of epigenetic silencing and activation to identify and carry out a comprehensive multi-omics analysis of cells undergoing epigenetic reprogramming during caudal fin regeneration. EpiTag GFP expression is transiently activated in cells contributing to regeneration between 12 to 16 hours post amputation (hpa), preceding the expression of canonical blastema markers. Single-cell RNA-seq reveals that GFP+ cells are restricted to regeneration-competent lineages such as pre-osteoblasts, proliferating cells, and wound epithelium. Integrated bulk RNA-seq, time-course RNA-seq, ATAC-seq, and bisulfite-seq on FACS-isolated GFP+ cells uncovers an early gene expression module enriched for chromatin regulators and a late gene expression module enriched for morphogenesis genes. Chromatin accessibility and DNA methylation changes are strongly associated with these late-expressed genes, suggesting epigenetic priming. We identify a number of epigenetic factors upregulated in the early gene expression module and show that ruvbl1 and ruvbl2, components of ATP-dependent chromatin remodeling complexes, are required for proper regeneration in both adult fins and larval tails. Our results establish EpiTag transgenics as a powerful in vivo tool for studying epigenetic reprogramming and highlight early chromatin remodeling events that enable activation of regenerative gene expression programs.