Axolotl (Ambystoma mexicanum) and the zebrafish (Danio rerio) represent organisms extensively studied because of their remarkable capability of fully regenerating completely functional tissues after a traumatic event takes place. However, the research conducted with regards to the genomics of these two organisms has remained fairly independent of each other. The intent of this study is to bridge this gap and connect genes between axolotl and the zebrafish by use a “Rosetta stone” framework to develop a database comparing gene expression data obtained from both microarraybased experiments and high-throughput DNA sequencing of axolotl and zebrafish mRNA and miRNA. Using gene data of this variety, accessed from a variety of private and public resources, 78 axolotl genes were matched to human genes and found to have homologous zebrafish genes. The function of these genes were organized and discussed from a variety of perspectives, including general gene ontologies, specific mechanisms and functions, expression during regeneration at specific times post amputation, and expression in normal regenerating specimens as compared to specimens exposed to the toxin TCDD. Specific proteins and protein functionalities that appear most frequently or novel significance included ribosomal proteins and mitochondrial processes, neurite regeneration, the presences of proteins NADH ubiquinone oxidoreductase, histone, cystatin, and cathepsin, cell differentiation, apoptosis and cellular maintenance, and the structure of the extracellular matrix.
Bolinger, Justin, "A Comparative Genomics Approach to Using High-Throughput Gene Expression Data to Study Limb Regeneration in Ambystoma Mexicanum and Danio Rerio: Developing a More Completely Annotated Database" (2013). Honors College. 116.