Abstract
There is a lack of understanding surrounding the molecular mechanisms involved in the development of chicken skeletal muscle in the late postnatal stage, especially in the regulation of breast muscle development related genes, pathways, miRNAs and other factors. In this study, 12 cDNA libraries and 4 small RNA libraries were constructed from Gushi chicken breast muscle samples from 6, 14, 22, and 30 weeks. A total of 15,508 known transcripts, 25,718 novel transcripts, 388 known miRNAs and 31 novel miRNAs were identified by RNA-seq in breast muscle at the four developmental stages. Through correlation analysis of miRNA and mRNA expression profiles, it was found that 417, 370, 240, 1,418, 496, and 363 negatively correlated miRNA–mRNA pairs of W14 vs. W6, W22 vs. W6, W22 vs. W14, W30 vs. W6, W30 vs. W14, and W30 vs. W22 comparisons, respectively. Based on the annotation analysis of these miRNA–mRNA pairs, we constructed the miRNA–mRNA interaction network related to biological processes, such as muscle cell differentiation, striated muscle tissue development and skeletal muscle cell differentiation. The interaction networks for signaling pathways related to five KEGG pathways (the focal adhesion, ECM-receptor interaction, FoxO signaling, cell cycle, and p53 signaling pathways) and PPI networks were also constructed. We found that ANKRD1, EYA2, JSC, AGT, MYBPC3, MYH11, ACTC1, FHL2, RCAN1, FOS, EGR1, and FOXO3, PTEN, AKT1, GADD45, PLK1, CCNB2, CCNB3 and other genes were the key core nodes of these networks, most of which are targets of miRNAs. The FoxO signaling pathway was in the center of the five pathway-related networks. In the PPI network, there was a clear interaction among PLK1 and CDK1, CCNB2, CDK1, and GADD45B, and CDC45, ORC1 and MCM3 genes. These results increase the understanding for the molecular mechanisms of chicken breast muscle development, and also provide a basis for studying the interactions between genes and miRNAs, as well as the functions of the pathways involved in postnatal developmental regulation of chicken breast muscle.
Highlights
In chickens, breast muscle is a major contributor to skeletal muscle and is directly correlated with meat quantity and quality
To investigate the key mRNAs involved in chicken breast muscle development, we analyzed the differentially expressed genes (DEGs) at four developmental stages of breast muscle in Gushi chicken
To identify key molecular players in the development of chicken breast muscle, based on the annotations of the negatively correlated miRNA–mRNA pairs in expression level, we focused on some DEG-differentially expressed miRNAs (DEMs) interactions associated with muscle development (Figure 3)
Summary
Breast muscle is a major contributor to skeletal muscle and is directly correlated with meat quantity and quality. MiRNAs are endogenous non-coding RNAs that regulate gene expression at the post-transcriptional level by binding to the 3 -UTRs of target mRNAs. Many myogenic transcription factors and genes are regulated by various miRNAs. For instance, muscle differentiation-related miRNAs (MyomiRs) such as miR-1, miR-206, and miR-133, interact with myogenic genes, such as myogenin (MyoG), myogenic differentiation (MyoD), myogenic factor 5 (Myf5), myocyte enhancer factor 2 (MEF2) and paired box 7 (PAX7). Muscle differentiation-related miRNAs (MyomiRs) such as miR-1, miR-206, and miR-133, interact with myogenic genes, such as myogenin (MyoG), myogenic differentiation (MyoD), myogenic factor 5 (Myf5), myocyte enhancer factor 2 (MEF2) and paired box 7 (PAX7) These interactions play an important regulatory role in the biological processes involved in muscle development, such as muscle fiber type determination, muscle cell proliferation and differentiation, and skeletal muscle hypertrophy and atrophy (Nakasa et al, 2010; Moncaut et al, 2013; Badodi et al, 2015). MiR-222a and miR-126-5p inhibit the expression of their target genes cytoplasmic polyadenylation element-binding protein 3 (CPEB3) and fibroblast growth factor receptor 3 (FGFR3) in DF-1 cells, and they play roles in the regulation of embryonic muscle development and growth (Jebessa et al, 2018)
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