Systematic identification and differential expression profiling of MicroRNAs from white and red muscles of siniperca chuatsi

MicroRNAs (miRNAs) participate in the regulation of myogenesis and muscle physiological function. Most skeletal muscles in vertebrates contain a mixture of fibertypes. So far, the regulatory mechanism of the miRNA in terms of controlling muscle phenotype is poorly understood. In the present study, we use Siniperca chuatsi as a model system and demonstrate that miRNAs are involved in regulating the physiological processes and metabolism of different muscle fibers in vertebrates. The miRNA transcriptomes of the white muscle, red muscle, and five other tissues from Siniperca chuatsi were profiled using Solexa deep sequencing. We characterized 186 conserved miRNAs and 3 novel miRNAs from the two small RNA libraries of white and red muscles. Among the 155 miRNAs overlapped between the two libraries, we identified 60 significantly expressed miRNAs between the two types of muscle fibers. Using integrative miRNA target-prediction and network-analysis approaches, an interaction network of differentially expressed and muscle-related miRNAs and their putative targets were constructed. Sch-miR-181a-5p that could act to control the performance of the different muscle fiber types by targeting the myostatin gene was identified.