Identification of differences in microRNA transcriptomes between porcine oxidative and glycolytic skeletal muscles

Abstract

BackgroundMicroRNAs (miRNAs) are a type of non-coding small RNA ~22 nucleotides in length that regulate the expression of protein coding genes at the post-transcriptional level. Glycolytic and oxidative myofibers, the two main types of skeletal muscles, play important roles in metabolic health as well as in meat quality and production in the pig industry. Previous expression profile studies of different skeletal muscle types have focused on these aspects of mRNA and proteins; nonetheless, an explanation of the miRNA transcriptome differences between these two distinct muscles types is long overdue.ResultsHerein, we present a comprehensive analysis of miRNA expression profiling between the porcine longissimus doris muscle (LDM) and psoas major muscle (PMM) using a deep sequencing approach. We generated a total of 16.62 M (LDM) and 18.46 M (PMM) counts, which produced 15.22 M and 17.52 M mappable sequences, respectively, and identified 114 conserved miRNAs and 89 novel miRNA*s. Of 668 unique miRNAs, 349 (52.25%) were co-expressed, of which 173 showed significant differences (P < 0.01) between the two muscle types. Muscle-specific miR-1-3p showed high expression levels in both libraries (LDM, 32.01%; PMM, 20.15%), and miRNAs that potentially affect metabolic pathways (such as the miR-133 and -23) showed significant differences between the two libraries, indicating that the two skeletal muscle types shared mainly muscle-specific miRNAs but expressed at distinct levels according to their metabolic needs. In addition, an analysis of the Gene Ontology (GO) terms and KEGG pathway associated with the predicted target genes of the differentially expressed miRNAs revealed that the target protein coding genes of highly expressed miRNAs are mainly involved in skeletal muscle structural development, regeneration, cell cycle progression, and the regulation of cell motility.ConclusionOur study indicates that miRNAs play essential roles in the phenotypic variations observed in different muscle fiber types.

Prokaryotic expression, purification, polyclonal antibody preparation, and tissue distribution of porcine Six1

“…Mammalian skeletal muscles are generally classified as fast and slow types based on the ratio of slow-and fast-type muscle fibers (Schiaffino and Reggiani, 2011). EDL muscle and LL muscle are typical fast muscles, while SOL muscle and PM muscle are typical slow muscles (O'Connor et al, 2003;Wang et al, 2012;Liu et al, 2013). Here we have shown that pSix1 protein was most abundant in the EDL muscle and LL muscle, followed by the SOL muscle and PM muscle, while it could not be detected in other tissues.…”

Dynamic changes in genes related to glucose uptake and utilization during pig skeletal and cardiac muscle development

“…3), which confirmed the oxidative capacity of PMM. 12) Expression pattern of miRNAs involved in glucose metabolism during development…”

microRNA profiling in three main stages during porcine spermatogenesis

“…Based on previous studies by Li et.al [29,30], we divided the mappable reads into three groups with progressively decreasing confidence: (1) porcine known miRNAs (Supplementary file 2: Table S2.1), with both mature miRNAs and the precursors mapped to the pig genome; 212 porcine known pre-miRNAs generated 392 mature miRNAs. Additionally, 23 unknown miRNA*s were detected in our library due to the development of sequencing methods; (2) porcine novel miRNAs (Supplementary file 2: Table S2.2), 291pre-miRNAs that have not been mapped to known porcine pre-miRNAs, but are homologous to other known miRBase mammalian pre-miRNAs, which confirmed that most of the miRNAs are highly conserved across various species [31].…”

“…In order to determine the differential expression (DE) levels between libraries, the IDEG6 program [67] was used for the normalization calculation. A unique miRNA was considered to be significantly differentially expressed only when both Fisher exact test and Chi-squared 2×2 test resulted in a P value<0.001 [26,30]. Among the 710 co-expressed miRNAs, 418 were differentially expressed miRNAs (Supplementary file 3: Table S3.2, Supplementary file 7: Fig S2), including the top 26 expressed small RNAs.…”