Title |
Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema
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Published in |
PLoS Computational Biology, March 2013
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DOI | 10.1371/journal.pcbi.1002936 |
Pubmed ID | |
Authors |
Ron Stewart, Cynthia Alexander Rascón, Shulan Tian, Jeff Nie, Chris Barry, Li-Fang Chu, Hamisha Ardalani, Ryan J. Wagner, Mitchell D. Probasco, Jennifer M. Bolin, Ning Leng, Srikumar Sengupta, Michael Volkmer, Bianca Habermann, Elly M. Tanaka, James A. Thomson, Colin N. Dewey |
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. |
X Demographics
Geographical breakdown
Country | Count | As % |
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Switzerland | 1 | 33% |
France | 1 | 33% |
Germany | 1 | 33% |
Demographic breakdown
Type | Count | As % |
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Scientists | 2 | 67% |
Science communicators (journalists, bloggers, editors) | 1 | 33% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 5 | 2% |
United Kingdom | 2 | <1% |
Spain | 2 | <1% |
Slovakia | 1 | <1% |
Taiwan | 1 | <1% |
Mexico | 1 | <1% |
Portugal | 1 | <1% |
Russia | 1 | <1% |
Korea, Republic of | 1 | <1% |
Other | 2 | <1% |
Unknown | 219 | 93% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 61 | 26% |
Researcher | 50 | 21% |
Student > Master | 22 | 9% |
Student > Bachelor | 19 | 8% |
Professor > Associate Professor | 14 | 6% |
Other | 38 | 16% |
Unknown | 32 | 14% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 105 | 44% |
Biochemistry, Genetics and Molecular Biology | 68 | 29% |
Medicine and Dentistry | 7 | 3% |
Neuroscience | 6 | 3% |
Computer Science | 4 | 2% |
Other | 10 | 4% |
Unknown | 36 | 15% |