Insight into Liver lncRNA and mRNA Profiling at Four Developmental Stages in Ningxiang Pig

SIMPLE SUMMARY: The current study reveals the expression profiles and functional networks on messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) in the liver of Ningxiang piglets across four developmental stages (30, 90, 150, and 210 days after birth). Differentially expressed mRNAs (DEmRNAs) were upregulated at 30 days; however, most differentially expressed lncRNAs (DElncRNAs) were downregulated at 210 days. A complex interaction between mRNAs and lncRNAs was identified by Short Time-series Expression Miner (STEM) analysis and weighted gene co-expression network analysis (WGCNA), indicating that lncRNAs may be a critical regulatory element in mRNAs. STEM was used to identify significant temporal expression profiles and the genes associated with them and to compare the behavior of these genes across multiple conditions. WGCNA was used to study the biological networks based on pairwise correlations between variables. One particular mRNA profile 4 contained CAV1, PACSIN2, and CDC42, which are the target genes of lncRNAs in the same profile, suggesting the possible regulatory relationship between lncRNAs and mRNAs. ABSTRACT: Ningxiang pigs, a fat-type pig, are native to Ningxiang County in Hunan Province, with thousands of years of breeding history. This study aims to explore the expression profiles and functional networks on messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) in the liver. Liver tissue of Ningxiang piglets was collected at 30, 90, 150, and 210 days after birth (four development stages), and the mRNA and lncRNA expression was profiled. Compared to mRNA and lncRNA expression profiles, most differentially expressed mRNAs (DEmRNAs) were upregulated at 30 days; however, most DElncRNAs were downregulated at 210 days. Via Short Time-series Expression Miner (STEM) analysis and weighted gene co-expression network analysis (WGCNA), a complex interaction between mRNAs and lncRNAs was identified, indicating that lncRNAs may be a critical regulatory element for mRNAs. One module of genes in particular (module profile 4) was related to fibril organization, vasculogenesis, GTPase activator activity, and regulation of kinase activity. The mRNAs and lncRNAs in module profile 4 had a similar pattern of expression, indicating that they have functional and regulatory relationships. Only CAV1, PACSIN2, and CDC42 in the particular mRNA profile 4 were the target genes of lncRNAs in that profile, which shows the possible regulatory relationship between lncRNAs and mRNAs. The expression of these genes and lncRNAs in profile 4 was the highest at 30 days, and it is believed that these RNAs may play a critical role during the suckling period in order to meet the dietary requirements of piglets. In the lncRNA–mRNA co-expression network, the identified gene hubs and associated lncRNAs were shown to be involved in saccharide, lipid, and glucose metabolism, which may play an important role in the development and health of the liver. This result will lead to further investigation of liver lncRNA functions at various stages of development in Ningxiang pigs.