TY - JOUR T1 - Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema A1 - Stewart, Ron A1 - Rascón, Cynthia Alexander A1 - Tian, Shulan A1 - Nie, Jeff A1 - Barry, Chris A1 - Chu, Li-Fang A1 - Ardalani, Hamisha A1 - Wagner, Ryan J. A1 - Probasco, Mitchell D. A1 - Bolin, Jennifer M. A1 - Leng, Ning A1 - Sengupta, Srikumar A1 - Volkmer, Michael A1 - Habermann, Bianca A1 - Tanaka, Elly M. A1 - Thomson, James A. A1 - Dewey, Colin N. Y1 - 2013/03/07 N2 - Author Summary Salamanders 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, we 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. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 9 IS - 3 UR - https://doi.org/10.1371/journal.pcbi.1002936 SP - e1002936 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.1002936 ER -