ArticlePLoS computational biology2013
Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
80 citing papers in PubMed, 144 citations in OpenAlex.
- Dynamic control of cell state transitions during tissue morphogenesis.The EMBO journal · 2026Review
- Are axolotls resistant to cancer? Possible explanations.Molecular biology reports · 2026Review
- Article
- Comparative multi-omic analysis reveals conserved and derived mechanisms of fin and limb regeneration.Nature communications · 2026Article
- Unveiling axolotl transcriptome for tissue regeneration with high-resolution annotation via long-read sequencing.Computational and structural biotechnology journal · 2024Article
- Sall4 regulates downstream patterning genes during limb regeneration.Developmental biology · 2024Article
- Systemic and local lipid adaptations underlie regeneration in Drosophila melanogaster and Ambystoma mexicanum.NPJ Regenerative medicine · 2024Article
- Axolotl mandible regeneration occurs through mechanical gap closure and a shared regenerative program with the limb.Disease models & mechanisms · 2024Article
- The mRNA and microRNA Landscape of the Blastema Niche in Regenerating Newt Limbs.International journal of molecular sciences · 2024Article
- Brittle star genome provides information on the evolution of regeneration.Nature ecology & evolution · 2024Article
- The brittle star genome illuminates the genetic basis of animal appendage regeneration.Nature ecology & evolution · 2024Article
- hoxc12/c13 as key regulators for rebooting the developmental program in Xenopus limb regeneration.Nature communications · 2024Article
- Manipulating Myc for reparative regeneration.Frontiers in cell and developmental biology · 2024Review
- Article
- Limb blastema formation: How much do we know at a genetic and epigenetic level?The Journal of biological chemistry · 2023Review
- The salamander blastema within the broader context of metazoan regeneration.Frontiers in cell and developmental biology · 2023Review
- A Practical Guide for CRISPR-Cas9-Induced Mutations in Axolotls.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Now that We Got There, What Next?Methods in molecular biology (Clifton, N.J.) · 2023Article
- Rebuilding limbs, one cell at a time.Developmental dynamics : an official publication of the American Association of Anatomists · 2022Article
- The specialist in regeneration-the Axolotl-a suitable model to study bone healing?NPJ Regenerative medicine · 2022Article
20 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors at 5 institutions in 2 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.