Epigenetic Profiling of Zebrafish Fin Regeneration

The ability to regenerate after injury is quite astonishing, yet not all organisms share this ability. Mammalian genomes likely encode all gene products required to regenerate an amputated limb, yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. While the catalogue of defined cell dynamics and molecular factors in tissue regeneration is expanding, we know comparatively little of how genes involved in regenerative events are engaged upon injury, despite decades of research. Certain non-mammalian vertebrates like salamanders and zebrafish possess these instructions, which exist as cis-regulatory elements that can direct expression of their target genes during regeneration. To identify candidate tissue regeneration enhancer elements (TREEs) important for zebrafish fin regeneration, we performed ATAC-seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified tens of thousands of DNA regions from each sample type with dynamic accessibility during regeneration, and assigned these regions to proximal genes with corresponding changes in expression by RNA-seq. To determine the extent to which these profiles reveal bona fide TREEs, we tested the sufficiency and requirements of several sequences in stable transgenic lines and mutant lines with homozygous deletions. Our study generates a new resource for dissecting the regulatory mechanisms of appendage generation and reveals a range of requirements for individual TREEs in control of regeneration programs.