Abstract
Liver is an important metabolic organ of mammals. During each transitional period of life, liver metabolism is programmed by a complex molecular regulatory system for multiple physiological functions, many pathways of which are regulated by hormones and cytokines, nuclear receptors, and transcription factors. To gain a comprehensive and unbiased molecular understanding of liver growth and development in Ningxiang pigs, we analyzed the mRNA, microRNA (miRNA), and proteomes of the livers of Ningxiang pigs during lactation, nursery, and fattening periods. A total of 22,411 genes (19,653 known mRNAs and 2758 novel mRNAs), 1122 miRNAs (384 known miRNAs and 738 novel miRNAs), and 1123 unique proteins with medium and high abundance were identified by high-throughput sequencing and mass spectrometry. We show that the differences in transcriptional, post-transcriptional, or protein levels were readily identified by comparing different time periods, providing evidence that functional changes that may occur during liver development are widespread. In addition, we found many overlapping differentially expressed genes (DEGs)/differentially expressed miRNAs (DEMs)/differentially expressed proteins (DEPs) related to glycolipid metabolism in any group comparison. These overlapping DEGs/DEMs/DGPs may play an important role in functional transformation during liver development. Short Time-series Expression Miner (STEM) analysis revealed multiple expression patterns of mRNA, miRNA, and protein in the liver. Furthermore, several diverse key Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including immune defense, glycolipid metabolism, protein transport and uptake, and cell proliferation and development, were identified by combined analysis of DEGs and DGPs. A number of predicted miRNA–mRNA–protein pairs were found and validated by qRT-PCR and parallel reaction monitoring (PRM) assays. The results provide new and important information about the genetic breeding of Ningxiang pigs, which represents a foundation for further understanding the molecular regulatory mechanisms of dynamic development of liver tissue, functional transformation, and lipid metabolism.
Highlights
Metabolism of lipid in animals is highly dependent upon liver development and physiology (Liu et al, 2018)
In order to further understand the differentially expressed proteins (DEPs) in three key growth stages involved in regulating the liver function, only the adjacent time point to compare differences in protein Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, we found that compared with 30 days, the 90 days upregulated protein significantly enriched in the 63 regulation pathway, covers almost all of the liver function (Figure 4A)
We found high expression of some miRNAs known to be involved in liver development and fatty acid (FA) metabolism, such as ssc-miR-143-3p, ssc-miR-21-5p, and ssc-miR-148a-3p, etc. (Figure 6B)
Summary
Metabolism of lipid in animals is highly dependent upon liver development and physiology (Liu et al, 2018). Data from several mammalian studies suggest that microRNAs (miRNAs) play an important regulatory role in liver lipid metabolism. MiR-122, which is highly expressed in mammalian liver, inhibitions the expression of genes involved in cholesterol biosynthesis by targeting the regulation of cationic amino acid transporter 1 (CPT1α), thereby regulating liver fatty acid (FA) and cholesterol synthesis (Iliopoulos et al, 2010). Li H. et al (2016) found that fatty acid desaturase 1 (FADS1) was targeted by miR-365-3p, miR-2185p, miR-181a-5p, miR-181b-5p, miR-29a-3p, and miR-23b-3p, while fatty acid desaturase 2 (FADS2) was targeted by miR-30c1-3p, which was found in the study of differences in miRNA expression in liver of 20- and 30-week-old hens. Y. et al, 2017), affecting the accumulation of triglyceride (TG) in hepatocytes
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