Analyses of MicroRNA and mRNA Expression Profiles Reveal the Crucial Interaction Networks and Pathways for Regulation of Chicken Breast Muscle Development

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 <i>W14</i> vs. <i>W6</i>, <i>W22</i> vs. <i>W6</i>, <i>W22</i> vs. <i>W14</i>, <i>W30</i> vs. <i>W6</i>, <i>W30</i> vs. <i>W14</i>, and <i>W30</i> vs. <i>W22</i> 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 <i>ANKRD1</i>, <i>EYA2</i>, <i>JSC</i>, <i>AGT</i>, <i>MYBPC3</i>, <i>MYH11</i>, <i>ACTC1</i>, <i>FHL2</i>, <i>RCAN1</i>, <i>FOS</i>, <i>EGR1</i>, and <i>FOXO3</i>, <i>PTEN</i>, <i>AKT1</i>, <i>GADD45</i>, <i>PLK1</i>, <i>CCNB2</i>, <i>CCNB3</i> 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 <i>PLK1</i> and <i>CDK1</i>, <i>CCNB2</i>, <i>CDK1</i>, and <i>GADD45B</i>, and <i>CDC45</i>, <i>ORC1</i> and <i>MCM3</i> 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.