Expression profiles of microRNAs in skeletal muscle of sheep by deep sequencing

Abstract

Objective MicroRNAs are a class of endogenous small regulatory RNAs that regulate cell proliferation, differentiation and apoptosis. Recent studies on miRNAs are mainly focused on mice, human and pig. However, the studies on miRNAs in skeletal muscle of sheep are not comprehensive. Methods RNA-seq technology was used to perform genomic analysis of miRNAs in prenatal and postnatal skeletal muscle of sheep. Targeted genes were predicted using miRanda software and miRNA-mRNA interactions were verified by quantitative real-time polymerase chain reaction. To further investigate the function of miRNAs, candidate targeted genes were enriched for analysis using gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment. Results The results showed total of 1,086 known miRNAs and 40 new candidate miRNAs were detected in prenatal and postnatal skeletal muscle of sheep. In addition, 345 miRNAs (151 up-regulated, 94 down-regulated) were differentially expressed. Moreover, miRanda software was performed to predict targeted genes of miRNAs, resulting in a total of 2,833 predicted targets, especially miR-381 which targeted multiple muscle-related mRNAs. Furthermore, GO and KEGG pathway analysis confirmed that targeted genes of miRNAs were involved in development of skeletal muscles. Conclusion This study supplements the miRNA database of sheep, which provides valuable information for further study of the biological function of miRNAs in sheep skeletal muscle.

RNA-Seq Reveals miRNA Role Shifts in Seven Stages of Skeletal Muscles in Goat Fetuses and Kids

“…With the development of sequencing technology, it is found that miRNAs in animal transcriptomes are more abundant than previously thought. There are now thousands of such molecules in skeletal muscles of many species, such as humans (Horak et al, 2016), sheep (Liu et al, 2019), and goat (Guo et al, 2016). Horak et al (2016) reviewed several representative miRNAs found in basic research and sequencing that were specifically expressed in skeletal muscle and played an important role in proliferation, differentiation, and regeneration, including miR-1, miR-133a, miR-133b, miR-206, miR-208b, miR-486, and miR-499.…”

“…These miRNAs are DEmiRNAs in this study. Liu et al (2019) analyzed the GO and KEGG enrichment terms for the 345 DEmiRNAs of sheep's longissimus dorsi between fetuses and adults and showed the regulatory network of 29 DEmiRNAs and 298 target genes. In addition, Wang et al (2014) revealed the expression profiles of goat miRNAs in the fetal and 6-month-old stages, identified 336 DEmiRNAs, and found that miR-424-5p and miR-29a may regulate muscle development.…”

Differential expression of miRNAs in skeletal muscles of Indian sheep with diverse carcass and muscle traits

“…Myomirs, oar-miR-1 and oar-miR-206 were over-expressed while oar-miR-133b and oar-miR-486 showed lower expression in Bandur sheep. Table 2 lists the miRNAs differentially expressed in Bandur that are known to be associated with muscle growth and development in sheep 11 .…”

“…Knowledge of miRNAs in skeletal muscles of various livestock species provides the possibility of identifying key regulators of muscle traits that can be used as biomarkers 21,31 . Several studies have identified and profiled miRNAs in the skeletal muscles of sheep 11,12 . However, there is dearth of information on molecular regulators for meat type sheep in India.…”

“…Their role in muscle cell proliferation and development has been well established 3 , 4 . Several reports are available describing the miRNA expression in skeletal muscles of cattle 5 , 6 , pig 7 , goat 8 , 9 and sheep 10 , 11 . Such studies have contributed to a better understanding of the regulatory role of miRNAs in muscling traits.…”