Abstract
Simple SummaryThe 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. 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.
Highlights
There are about 20,000 protein-coding genes in the human genome, accounting for less than 2% of the whole genome [1]
The majority of long non-coding RNAs (lncRNAs) contained two exons, followed by three exons, and were lower and shorter than messenger RNAs (mRNAs) in terms of the expression level and length, which is consistent with previous results in humans and mammals (Figure 1B–E) [16]
Among the common mRNAs, we discovered that ACSL3, CES1, CYP2C42, CYP4A24, and PLIN4 were associated with fatty acid metabolism, indicating that it is an important part of liver development (Table S4)
Summary
There are about 20,000 protein-coding genes in the human genome, accounting for less than 2% of the whole genome [1]. Those sequences that do not encode proteins were once thought to be "junk sequences" or “noise” [2]. The long non-coding RNA (lncRNAs), a group of RNA molecules with a transcript length of more than 200 bp, are structurally like mRNAs, but cannot encode proteins [4]. Recent research has shown that lncRNAs can regulate gene expression as key regulatory molecules at the transcriptional and post-transcriptional level and play a significant biological role in mammalian physiological and pathological processes [4,5]. As more lncRNAs are identified in humans and mammals, their regulatory relationship with corresponding potential target genes remains unclear, especially concerning the effects on fatty acid biosynthesis, transport, and metabolism
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