RNA-seq data characterization of transcriptional dynamics during salamander limb regeneration

AxolotlSalamanders such as the axolotl can fully regenerate a limb upon amputation, making them the vertebrate champions of regeneration. On the other hand, humans and other mammals possess a very limited ability to regenerate limb structures. Learning about the genes, gene networks, and pathways activated in the salamander during limb regeneration will provide cues to improving the regenerative response in mammals. Elucidating these genes, networks, and pathways is difficult, however, because the axolotl does not yet have its genome sequenced and because it has diverged evolutionarily from species with a sequenced genome.

Here, a team led by researchers at the Morgridge Institute for Research produce a set of gene transcripts via RNA sequencing (RNA-seq) for the axolotl and provide information on the nature of the genes activated during regeneration. To determine the identity of these axolotl genes, we use comparative transcriptomics techniques to match the axolotl transcript data to that of the well-annotated human gene set. Supporting previous studies, we find upregulation of many genes previously found to be involved in limb development and regeneration. In addition, we find a burst of cancer-related genes during the first phase of regeneration and identify a set of genes previously not associated with the regeneration process.

  • Stewart R, Rascón CA, Tian S, Nie J, Barry C, et al. (2013) Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema. PLoS Comput Biol 9(3), e1002936. [article]