PSII-11 RNA sequencing analysis reveals differentially expressed genes and novel upstream transcriptional regulators in porcine longissimus dorsi muscle affected by dietary lysine restriction

Abstract

Abstract The objective of this research was to investigate the effects of dietary lysine restriction on the global gene expression of skeletal muscle in growing pigs. Twelve crossbred (Yorkshire × Landrace) barrows (initial BW 22.6 ± 2.04 kg) were randomly assigned to two dietary treatments (Diet I: a lysine-deficient diet; Diet II: a lysine-adequate diet) according to a completely randomized experiment design (n = 6). After feeding for 8 weeks, muscle samples were collected from longissimus dorsi of individual pigs (approximately 2 g/each). The total RNA isolated was used to prepare cDNA library for RNA sequencing (RNA-Seq) analysis. The RNA-Seq data was then analyzed using the CLC Genomics Workbench to identify differentially expressed genes (DEGs). Sixty-nine genes were found differentially expressed (Benjamin-Hochberg corrected P < 0.05) in Diet I vs. Diet II pigs, of which 29 genes were down-regulated (Log₂ fold change (FC) < - 0.58) and 40 genes were up-regulated (Log₂ FC > 0.58). Gene ontology (GO) analysis of these DEGs for functional annotation using DAVID found a total of 36 GO terms. The significantly enriched terms (Benjamin-Hochberg corrected P < 0.05) are associated with biological processes that include acute-phase response, platelet activation, and protein polymerization, and Molecular Functions that include serine-type endopeptidase inhibitor activity, small molecule binding, heme binding, and oxidoreductase activity. In addition, Ingenuity Pathway Analysis predicted some upstream transcriptional regulators that regulate several sets of DEGs. For example, lysine restriction may lead inhibition of insulin, EIF2AK4 (an eIF2α activator), and MYC (a transcript elongation factor), which are associated with the regulation of protein synthesis. It may also lead activation of STAT3 and HNF1A, which regulate cell movement and fatty acid metabolism, respectively. In summary, these novel results showed that dietary lysine restriction may compromise pig muscle protein synthesis through the aforementioned transcriptional regulators and their affected genes.