ZFIN ID: ZDB-PUB-200716-2
Identification and requirements of enhancers that direct gene expression during zebrafish fin regeneration
Thompson, J.D., Ou, J., Lee, N., Shin, K., Cigliola, V., Song, L., Crawford, G.E., Kang, J., Poss, K.D.
Date: 2020
Source: Development (Cambridge, England)   147(14): (Journal)
Registered Authors: Cigliola, Valentina, Kang, Junsu, Lee, Nutishia, Ou, Jianhong, Poss, Kenneth D., Thompson, John D.
Keywords: Chromatin, Enhancers, Fin regeneration, Genome-wide profiling, Regeneration, Zebrafish
Microarrays: GEO:GSE146960
MeSH Terms:
  • Animal Fins/metabolism*
  • Animal Fins/physiology
  • Animals
  • Animals, Genetically Modified/metabolism
  • Chromatin/metabolism
  • Chromatin Assembly and Disassembly
  • Connexin 43/genetics
  • Connexin 43/metabolism
  • Enhancer Elements, Genetic/genetics*
  • Fibroblast Growth Factors/genetics
  • Fibroblast Growth Factors/metabolism
  • Fibroblasts/cytology
  • Fibroblasts/metabolism
  • Gene Expression
  • Leptin/genetics
  • Leptin/metabolism
  • Midkine/genetics
  • Midkine/metabolism
  • Regeneration/physiology*
  • Regulatory Sequences, Nucleic Acid/genetics
  • Zebrafish/metabolism*
  • Zebrafish Proteins/genetics
  • Zebrafish Proteins/metabolism
PubMed: 32665240 Full text @ Development
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 expression changes by RNA-seq. To determine whether 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. These experiments validated new non-coding regulatory sequences near induced and/or essential genes during fin regeneration, including fgf20a, mdka, and cx43, identifying distinct domains of directed expression for each confirmed TREE. Whereas deletion of the previously identified LEN enhancer abolished detectable induction of the nearby leptin b gene during regeneration, deletions of enhancers linked to fgf20a, mdka, and cx43 had no effect or partially reduced gene expression. 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.