A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors

Cell Rep. 2017 Jan 17;18(3):762-776. doi: 10.1016/j.celrep.2016.12.063.


Mammals have extremely limited regenerative capabilities; however, axolotls are profoundly regenerative and can replace entire limbs. The mechanisms underlying limb regeneration remain poorly understood, partly because the enormous and incompletely sequenced genomes of axolotls have hindered the study of genes facilitating regeneration. We assembled and annotated a de novo transcriptome using RNA-sequencing profiles for a broad spectrum of tissues that is estimated to have near-complete sequence information for 88% of axolotl genes. We devised expression analyses that identified the axolotl orthologs of cirbp and kazald1 as highly expressed and enriched in blastemas. Using morpholino anti-sense oligonucleotides, we find evidence that cirbp plays a cytoprotective role during limb regeneration whereas manipulation of kazald1 expression disrupts regeneration. Our transcriptome and annotation resources greatly complement previous transcriptomic studies and will be a valuable resource for future research in regenerative biology.

Keywords: Trinity; Trinotate; axolotl; blastema; cirbp; expression analysis; kazald1; limb; regeneration; transcriptome.

MeSH terms

  • Ambystoma mexicanum
  • Animals
  • Extremities / physiology*
  • In Situ Hybridization
  • Insulin-Like Growth Factor Binding Proteins / antagonists & inhibitors
  • Insulin-Like Growth Factor Binding Proteins / genetics
  • Insulin-Like Growth Factor Binding Proteins / metabolism
  • RNA / chemistry
  • RNA / metabolism
  • RNA Interference
  • RNA Splicing
  • RNA, Small Interfering / metabolism
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism
  • Regeneration
  • Sequence Analysis, RNA
  • Transcriptome*


  • Insulin-Like Growth Factor Binding Proteins
  • RNA, Small Interfering
  • RNA-Binding Proteins
  • RNA