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PLoS Comput Biol. 2013;9(3):e1002936. doi: 10.1371/journal.pcbi.1002936. Epub 2013 Mar 7.

Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema.

Author information

1
Regenerative Biology, Morgridge Institute for Research, Madison, Wisconsin, United States of America. rstewart@morgridgeinstitute.org

Abstract

The salamander has the remarkable ability to regenerate its limb after amputation. Cells at the site of amputation form a blastema and then proliferate and differentiate to regrow the limb. To better understand this process, we performed deep RNA sequencing of the blastema over a time course in the axolotl, a species whose genome has not been sequenced. Using a novel comparative approach to analyzing RNA-seq data, we characterized the transcriptional dynamics of the regenerating axolotl limb with respect to the human gene set. This approach involved de novo assembly of axolotl transcripts, RNA-seq transcript quantification without a reference genome, and transformation of abundances from axolotl contigs to human genes. We found a prominent burst in oncogene expression during the first day and blastemal/limb bud genes peaking at 7 to 14 days. In addition, we found that limb patterning genes, SALL genes, and genes involved in angiogenesis, wound healing, defense/immunity, and bone development are enriched during blastema formation and development. Finally, we identified a category of genes with no prior literature support for limb regeneration that are candidates for further evaluation based on their expression pattern during the regenerative process.

PMID:
23505351
PMCID:
PMC3591270
DOI:
10.1371/journal.pcbi.1002936
[Indexed for MEDLINE]
Free PMC Article

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