Transcriptome sequencing analysis of the role of miR-499-5p and SOX6 in chicken skeletal myofiber specification

Abstract

MicroRNAs (miRNAs) might play critical roles in skeletal myofiber specification. In a previous study, we found that chicken miR-499-5p is specifically expressed in slow-twitch muscle and that its potential target gene is SOX6. In this study, we performed RNA sequencing to investigate the effects of SOX6 and miR-499-5p on the modulation and regulation of chicken muscle fiber type and its regulatory mechanism. The expression levels of miR-499-5p and SOX6 demonstrated opposing trends in different skeletal muscles and were associated with muscle fiber type composition. Differential expression analysis revealed that miR-499-5p overexpression led to significant changes in the expression of 297 genes in chicken primary myoblasts (CPMs). Myofiber type-related genes, including MYH7B and CSRP3, showed expression patterns similar to those in slow-twitch muscle. According to functional enrichment analysis, differentially expressed genes were mostly associated with muscle development and muscle fiber-related processes. SOX6 was identified as the target gene of miR-499-5p in CPM using target gene mining and luciferase reporter assays. SOX6 knockdown resulted in upregulation of the slow myosin genes and downregulation of fast myosin genes. Furthermore, protein-protein interaction network analysis revealed that MYH7B and RUNX2 may be the direct targets of SOX6. These results indicated that chicken miR-499-5p may promote slow-twitch muscle fiber formation by repressing SOX6 expression. Our study provides a dataset that can be used as a reference for animal meat quality and human muscle disease studies.

MiR-106a-5p by Targeting MAP3K2 Promotes Repair of Oxidative Stress Damage to the Intestinal Barrier in Prelaying Ducks

“…MiRNAs are endogenous small noncoding RNAs that have been shown to be involved in various cellular processes, including proliferation, differentiation, migration, invasion, and apoptosis, according to numerous studies [28,29]. Importantly, miRNAs play a pivotal role in the repair of oxidative stress damage to the intestinal barrier [30][31][32]. In our study, miRNA sequencing analysis revealed 21 differentially expressed miRNAs in the intestines of cage-reared ducks compared to those in the traditional breeding group.…”

Research progress on regulating factors of muscle fiber heterogeneity in poultry: a review

“…These miRNAs target SOX6, a repressor of slow muscle-specific gene expression, and CALM1, a key component of cGMP-PKG and calcium signaling pathways, respectively, to regulate the formation of slow muscle fibers. Recent transcriptome sequencing analysis also confirms this conclusion at the omics level ( Liu et al, 2022 ). One such regulator, miR-499-5p, is a well-known positive regulator for type I muscle fibers across species and has been found to influence muscle fiber type transformation in chickens by targeting multiple genes, including cysteine and glycine protein 3 ( CSRP3 ) and calpain 3 ( CAPN3 ) ( Felício et al, 2013 ).…”

“…Furthermore, circPTPN4, a recently identified circular RNA, functions as a molecular sponge for miR-499-3p, inhibiting mitochondrial biogenesis and activating the phenotype characteristic of fast-twitch muscles ( Cai et al, 2022 ). Over the past three years, multi-omics sequencing studies focusing on oxidative and glycolytic muscle fibers in poultry have revealed numerous potential regulators ( Liu et al, 2020 ; Wang et al, 2020 ; Ju et al, 2021 ; Liu et al, 2022 ) However, most of these findings require validation at the single-cell level to fully understand their roles and mechanisms in muscle fiber type regulation.…”

Molecular mechanisms underlying the impact of muscle fiber types on meat quality in livestock and poultry

“…Notably, miR-499 has been unvealed to negatively regulate the formation of fast-twitch muscle, inhibited the formation of fast-twitch muscle fibers through repressing the expression of Sox6 (Figure 3) (77). It has been found that the knockout of Sox6 can induce remodeling of muscle fiber types and effectively regulate muscle metabolism (79). Furthermore, deeper exploration has demonstrated that Sox6 directly inhibits the transcription of genes related to slow-twitch muscle fiber by binding to the conserved cis-regulatory elements (46).…”