Identification and Profiling of microRNAs and Their Target Genes from Developing Caprine Skeletal Muscle

Abstract

Goat is an important agricultural animal for meat production. Functional studies have demonstrated that microRNAs (miRNAs) regulate gene expression at the post-transcriptional level and play an important role in various biological processes. Although studies on miRNAs expression profiles have been performed in various animals, relatively limited information about goat muscle miRNAs has been reported. To investigate the miRNAs involved in regulating different periods of skeletal muscle development, we herein performed a comprehensive research for expression profiles of caprine miRNAs during two developmental stages of skeletal muscles: fetal stage and six month-old stage. As a result, 15,627,457 and 15,593,721 clean reads were obtained from the fetal goat library (FC) and the six month old goat library (SMC), respectively. 464 known miRNAs and 83 novel miRNA candidates were identified. Furthermore, by comparing the miRNA profile, 336 differentially expressed miRNAs were identified and then the potential targets of the differentially expressed miRNAs were predicted. To understand the regulatory network of miRNAs during muscle development, the mRNA expression profiles for the two development stages were characterized and 7322 differentially expressed genes (DEGs) were identified. Then the potential targets of miRNAs were compared to the DEGs, the intersection of the two gene sets were screened out and called differentially expressed targets (DE-targets), which were involved in 231 pathways. Ten of the 231 pathways that have smallest P-value were shown as network figures. Based on the analysis of pathways and networks, we found that miR-424-5p and miR-29a might have important regulatory effect on muscle development, which needed to be further studied. This study provided the first global view of the miRNAs in caprine muscle tissues. Our results help elucidation of complex regulatory networks between miRNAs and mRNAs and for the study of muscle development.

Identification and Expression Profiling of miRNAome in Goat longissimus dorsi Muscle from Prenatal Stages to a Neonatal Stage

“…In this work, a total of 410 known goat miRNAs and 752 goat miRNA homologs were identified across the four developmental stages studied. Some of the expressed miRNAs identified here have already been reported in different species [3, 14, 16, 21, 38], indicating similar molecular mechanisms underlying skeletal muscle development in animals. For instance, eleven and nine of the most abundant miRNAs (over 10000 RPM), including the myomiRs, were among the top 20 abundantly expressed miRNAs detected during skeletal muscle development in porcine [14] and Xuhuai goat [21], respectively.…”

“…Previous studies in livestock have demonstrated that many miRNAs are highly expressed in prenatal stages and thus are thought to play important roles in skeletal myogenesis [12, 14, 16, 21]. In this work, a total of 410 known goat miRNAs and 752 goat miRNA homologs were identified across the four developmental stages studied.…”

“…Although advances have been made regarding the actions of miRNAs during goat [21] and sheep [15, 37] myogenesis, the expression landscape of miRNAs during goat skeletal muscle development remains poorly understood. Accordingly, in order to provide new sights into the functions of miRNAs during goat skeletal development, we systematically identified the miRNAs that regulate goat skeletal myogenesis, and examined their temporal expression profiles in longissimus dorsi muscle from an early prenatal stage to a neonatal stage.…”

“…However, the number of goat miRNA sequences in miRBase is much lower compared to the data deposition of miRNAs for pig and cattle. Wang et al [21] recently examined the genome-wide expression profiles of miRNAs and their interactions with mRNAs in the Xuhuai goat. They used Longissimus thoracis samples from a 90-day fetus and a six month-old goat, and their results suggested miRNAs to play important roles during goat skeletal muscle development.…”

Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat

“…In goat skeletal muscle, the main focus has been on genes and miRNAs rather than on lncRNAs [44, 45, 50, 51]. In the present study, we identified a total of 3981 multiple exon lncRNAs in fetal and postnatal goat skeletal muscle.…”