Oncorhynchus mykiss pax7 sequence variations with comparative analyses against other teleost species

Abstract

The paired box-7 (pax7) transcription factor expressed in satellite cells (SCs) is an essential regulator of skeletal muscle growth and regeneration in vertebrates including fish. Characterization of rainbow trout (Oncorhynchus mykiss) pax7 gene/s may offer novel insights into skeletal myogenesis by SCs in this indeterminate growth species. Further, evaluation of promoters for cis-regulatory regions may shed light on the evolutionary fate of the duplicated genes. Employing standard PCR, cloning and computational approach, we identified and report complete coding sequences of two pax7 paralogs of rainbow trout (rt); rtpax7α and rtpax7β. Both genes show significant identity in the nucleotide (97%) and the predicted amino acid (98%) sequences, and bear the characteristic paired domain (PD), octapeptide (OP) and homeodomain (HD) motifs. We further report several splice variants of each gene and nucleotide differences in coding sequence that predicts six putative amino acid changes between the two genes. Additionally, we noted a trinucleotide deletion in rtpax7β that results in putative serine elimination at the N-terminus and a single nucleotide polymorphism (SNP) in majority of the rtpax7β variants (6/10) that predicts an arginine substitution for a lysine. We also deciphered the genomic organization up to the first three exons and the upstream putative promoter regions of both genes. Comparative in silico analysis of both the trout pax7 promoters with that of zebrafish pax7 duplicates; zfpax7a and zfpax7b; predicts several important cis-elements/transcription factor binding sites (TFBS) in these teleost pax7 promoter regions.