Integration Analysis of lncRNA Regulatory Network Involving miRNA and mRNA in Chicken Breast Muscle

Chicken growth is a complex quantitative trait controlled by multiple genes, but currently little is known of its epigenetic regulatory mechanism. In this study, we identified long noncoding RNA (lncRNA) and mRNA expression profiles from the breast muscle of 7-week-old White Recessive Rock (WRR) and Xinghua (XH) chickens by RNA-seq. A total of 2,636 and 2,651 lncRNAs were identified in WRR and XH, respectively. Among the 239 differentially expressed lncRNAs identified, 52 were down-regulated and 187 were up-regulated in WRR when compared to XH. Moreover, we identified differentially expressed genes around 100 Kb upstream and downstream of differentially expressed lncRNAs to determine potential lncRNA“cis” genes. A total of 88 lncRNA-mRNA pairs were involved in the cis-regulation network. Ingenuity pathway analysis (IPA) showed that the target “cis” genes of lncRNAs were involved in the insulin receptor signaling pathway that controls critical energy functions such as glucose and lipid metabolism. Using our previous miRNA data, we further performed integration analysis of lncRNA-miRNA-mRNA interaction acting as competing endogenous RNAs(ceRNAs). The lncRNA-miRNA-mRNA network includes two interactions: one between miRNAs and mRNA targets, and the other between miRNA and lncRNA targets. The LncRNA-miRNA-mRNA network was consisted of 373 negatively regulated miRNA-mRNA pairs and 483 negatively regulated miRNA-lncRNA pairs. This network contains some muscle growth related lncRNA-miRNA-mRNA pairs, such as lncRNA08384-miR-16-5p-IRS1 pairs, and lncRNA16255-miR-30a-5p-FOXO3 pairs. In summary, the predicted lncRNA regulatory network involving miRNA and mRNA provides important information for us to further study the epigenetic mechanism of muscle growth and differentiation in chicken.