@article{10.1371/journal.pcbi.1002936, doi = {10.1371/journal.pcbi.1002936}, author = {Stewart, Ron AND Rascón, Cynthia Alexander AND Tian, Shulan AND Nie, Jeff AND Barry, Chris AND Chu, Li-Fang AND Ardalani, Hamisha AND Wagner, Ryan J. AND Probasco, Mitchell D. AND Bolin, Jennifer M. AND Leng, Ning AND Sengupta, Srikumar AND Volkmer, Michael AND Habermann, Bianca AND Tanaka, Elly M. AND Thomson, James A. AND Dewey, Colin N.}, journal = {PLOS Computational Biology}, publisher = {Public Library of Science}, title = {Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema}, year = {2013}, month = {03}, volume = {9}, url = {https://doi.org/10.1371/journal.pcbi.1002936}, pages = {1-15}, 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.}, number = {3}, }