In Silico Identification of Putative Muscle Adaptation-Associated MicroRNAs and Analysis of their Gene Targets' Molecular Network During Voluntary Wheel Running in Mus musculus

Abstract

DNA sequence of 62 up-regulated and 214 down-regulated clones, obtained from transcriptional profiling of mouse skeletal muscle following 5-10 days of voluntary wheel running experiment of Takemasa el al., were retrieved from GenBank’s Expressed Sequence Tags (EST) database. A homology search between the EST sequences and microRNA (miRNAs) sequences available in the miRBase Sequence database was done, obtaining 20 EST sequences (one up- regulated clone and nineteen down-regulated clones) carrying mature miRNA homologs. Using mfold, secondary structure and thermodynamic details of the 20 ESTs were determined. Four ESTs carrying putative miRNA precursor passed the criteria created by Ambros el al. for miRNA annotation. MiRNA X, a homolog of mmu-miR-709, has a MFE of -23.8 kcal/mol and a MFEI of 0.61. MiRNA W, Y and Z are orthologs of mmu-miR-574-5p. These miRNAs have a MFE of -29.6 kcal/mol, -35.2 kcal/mol, -42.8 kcal/mol and MFEI of 0.85, 1.135, and 1.157, respectively. Gene targets of mmu-miR-709 and mmu-miR-574-5p were obtained from miRBase Target Database (miRanda list). Gene targets were narrowed down using UniProt, limiting the search to annotated target genes present in mice skeletal muscles. The UniProt search yielded 43 gene targets for mmu-miR-709 and 37 for mmu-miR-574-5p. The Ingenuity Pathways Analysis (IPA) program was used to generate seven interactome networks for gene targets of each miRNA. The top scoring molecular network of the gene targets for each miRNA was further analyzed. It was found that certain genes in the mouse skeletal muscle cells maintaining normal molecular functions in the muscle cells are up- or down- regulated during exercise, with miRNAs possibly playing a role in the process.