Deep Small RNA Sequencing Reveals Important miRNAs Related to Muscle Development and Intramuscular Fat Deposition in Longissimus dorsi Muscle From Different Goat Breeds

Abstract

MicroRNAs (miRNAs) are a class of small non-coding RNAs that have been shown to play important post-transcriptional regulatory roles in the growth and development of skeletal muscle tissues. However, limited research into the effect of miRNAs on muscle development in goats has been reported. In this study, Liaoning cashmere (LC) goats and Ziwuling black (ZB) goats with significant phenotype difference in meat production performance were selected and the difference in Longissimus dorsi muscle tissue expression profile of miRNAs between the two goat breeds was then compared using small RNA sequencing. A total of 1,623 miRNAs were identified in Longissimus dorsi muscle tissues of the two goat breeds, including 410 known caprine miRNAs, 928 known species-conserved miRNAs and 285 novel miRNAs. Of these, 1,142 were co-expressed in both breeds, while 230 and 251 miRNAs were only expressed in LC and ZB goats, respectively. Compared with ZB goats, 24 up-regulated miRNAs and 135 miRNAs down-regulated were screened in LC goats. A miRNA-mRNA interaction network showed that the differentially expressed miRNAs would target important functional genes associated with muscle development and intramuscular fat deposition. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the target genes of differentially expressed miRNAs were significantly enriched in Ras, Rap 1, FoxO, and Hippo signaling pathways. This study suggested that these differentially expressed miRNAs may be responsible for the phenotype differences in meat production performance between the two goat breeds, thereby providing an improved understanding of the roles of miRNAs in muscle tissue of goats.

MicroRNA-381 Regulates Proliferation and Differentiation of Caprine Skeletal Muscle Satellite Cells by Targeting PTEN and JAG2

“…In this context, SMSCs have been widely used as models for investigating the growth and development of skeletal muscle in various species [ 3 , 4 , 6 , 7 ]. In our previous study, miR-381 was identified as the most down-regulated miRNA (fold change = 20.0, p = 1.6 × 10 −8 ) in Liaoning cashmere goats with higher muscle fiber size and carcass weight compared to Ziwuling black goats [ 10 ]. It was therefore inferred that miR-381 may regulate the size of caprine muscle fiber by regulating the activities of SMSCs.…”

“…In our previous study, miR-381 was found to be the most down-regulated miRNA in skeletal muscle of Liaoning cashmere goats with higher meat yield and larger muscle fiber size, when compared to Ziwuling black goats [ 10 ]. For example, the carcass weight of Liaoning cashmere goats was 14.10 ± 1.17 kg, which was higher than that of Ziwuling black goats with a carcass weight of 7.45 ± 1.28 kg.…”

Characteristics and Expression of circ_003628 and Its Promoted Effect on Proliferation and Differentiation of Skeletal Muscle Satellite Cells in Goats

“…It was found that in the postnatal period of animals, increases of skeletal muscle mass mainly depend on the hypertrophy of muscle fibers, closely related to proliferation and differentiation of SMSCs [ 42 , 43 , 44 , 45 ]. In this study, si-circ_003628 decreased the expression levels of proliferation marker genes Pax7 , CDK2 , CDK4 and CyclinD1 .…”

Whole-transcriptome analyses of sheep embryonic testicular cells infected with the bluetongue virus

“…The miRNA raw data were processed through an in-house program, ACGTA101-miR (v4.2) (LC Science, USA) to remove adapter dimers, junk, low complexities, common RNA families (rRNA, tRNA, snRNA, and snoRNA), repeats, and sequences <18 nt or >26 nt in length were filtered out using Rfam (v13.0) and Repbase Update ( 28 , 29 ). The 18~26 nt unique reads were mapped to miRNA sequences in miRBase (v22.0) ( 30 ). Mapping was also performed on pre-miRNA against Ovis aries genomic data (GCA_000298735.1).…”

“…Mapping was also performed on pre-miRNA against Ovis aries genomic data (GCA_000298735.1). The unique sequences that aligned to the known miRNA sequences in miRBase (v22.0) were identified as known miRNAs ( 30 ). The secondary structure of pre-miRNAs was presented as a hairpin, including 5p- and 3p- derived miRNA.…”