Abstract
BackgroundThe differentiation of skeletal muscle-derived satellite cells (MDSCs) is important in controlling muscle growth, improving livestock muscle quality, and healing of muscle-related disease. MicroRNAs (miRNAs) are a class of gene expression regulatory factors, which play critical roles in the regulation of muscle cell differentiation. This study aimed to compare the expression profile of miRNAs in MDSC differentiation, and to investigate the miRNAs which are involved in MDSC differentiation.MethodTotal RNA was extracted from MDSCs at three different stages of differentiation (MDSC-P, MDSC-D1 and MDSC-D3, representing 0, 1 and 3 days after differentiation, respectively), and used to construct small RNA libraries for RNA sequencing (RNA-seq).ResultsThe results showed that in total 617 miRNAs, including 53 novel miRNA candidates, were identified. There were 9 up-expressed, 165 down-expressed, and 15 up-expressed, 145 down-expressed in MDSC-D1 and MDSC-D3, respectively, compared to those in MDSC-P. Also, 17 up-expressed, 55 down-expressed miRNAs were observed in MDSC-D3 compared to those in MDSC-D1. All known miRNAs belong to 237 miRNA gene families. Furthermore, we observed some sequence variants and base edits of the miRNAs. GO and KEGG pathway analysis showed that the majority of target genes regulated by miRNAs were involved in cellular metabolism, pathways in cancer, actin cytoskeleton regulation and the MAPK signaling pathway. Regarding the 53 novel miRNAs, there were 7 up-expressed, 31 down-expressed, and 8 up-expressed, 26 down-expressed in MDSC-D1 and MDSC-D3, respectively, compared to those in MDSC-P. The expression levels of 12 selected miRNA genes detected by RT-qPCR were consistent with those generated by deep sequencing.ConclusionsThis study confirmed the authenticity of 564 known miRNAs and identified 53 novel miRNAs which were involved in MDSC differentiation. The identification of novel miRNAs has significantly expanded the repertoire of bovine miRNAs and could contribute to advances in understanding muscle development in cattle.Electronic supplementary materialThe online version of this article (doi:10.1186/s11658-016-0009-x) contains supplementary material, which is available to authorized users.
Highlights
The differentiation of skeletal muscle-derived satellite cells (MDSCs) is important in controlling muscle growth, improving livestock muscle quality, and healing of muscle-related disease
Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the majority of target genes regulated by miRNAs were involved in cellular metabolism, pathways in cancer, actin cytoskeleton regulation and the MAPK signaling pathway
This study confirmed the authenticity of 564 known miRNAs and identified 53 novel miRNAs which were involved in MDSC differentiation
Summary
The differentiation of skeletal muscle-derived satellite cells (MDSCs) is important in controlling muscle growth, improving livestock muscle quality, and healing of muscle-related disease. MicroRNAs (miRNAs) are a class of gene expression regulatory factors, which play critical roles in the regulation of muscle cell differentiation. In the process of MDSC differentiation, progenitor cells first proliferate, exit from the cell cycle, and undergo differentiation, alignment, and fusion to form multinucleated myotubes [3,4,5]. These molecular events are orchestrated by myogenic regulatory factors and miRNAs. The miRNAs are a family of noncoding small RNAs, approximately 22 nucleotides in length. The miRNAs have been shown to play critical roles in skeletal muscle development and in regulation of muscle cell proliferation and differentiation [7]. MiR-27 could modulate the entry of cells into the myogenic differentiation program [11]
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