Nutrient supply affects the mRNA expression profile of the porcine skeletal muscle

Abstract

Background: The genetic basis of muscle fat deposition in pigs is not well known. So far, we have only identified a limited number of genes involved in the absorption, transport, storage and catabolism of lipids. Such information is crucial to interpret, from a biological perspective, the results of genome-wide association analyses for intramuscular fat content and composition traits. Herewith, we have investigated how the ingestion of food changes gene expression in the gluteus medius muscle of Duroc pigs.

Results: By comparing the muscle mRNA expression of fasted pigs (T0) with that of pigs sampled 5 h (T1) and 7 h (T2) after food intake, we have detected differential expression (DE) for 148 (T0-T1), 520 (T0-T2) and 135 (T1-T2) genes (q-value <0.05 and a |FC| > of 1.5). Many of these DE genes were transcription factors, suggesting that we have detected the coordinated response of the skeletal muscle to nutrient supply. We also found DE genes with a dual role in oxidative stress and angiogenesis (THBS1, THBS2 and TXNIP), two biological processes that are probably activated in the post-prandial state. Finally, we have identified several loci playing a key role in the modulation of circadian rhythms (ARNTL, PER1, PER2, BHLHE40, NR1D1, SIK1, CIART and CRY2), a result that indicates that the porcine muscle circadian clock is modulated by nutrition.

Conclusion: We have shown that hundreds of genes change their expression in the porcine skeletal muscle in response to nutrient intake. Many of these loci do not have a known metabolic role, a result that suggests that our knowledge about the genetic basis of muscle energy homeostasis is still incomplete.

Keywords: Angiogenesis; Circadian rhythm; Oxidative stress; Pig; RNA-seq; Transcription factor.

Fig. 1

Kinetics of the average concentrations of plasma glucose, cholesterol, triglycerides and non-esterified fatty acids (FA) in 8 Duroc pigs at four time points: before eating and 2, 4 and 6 h post-ingestion (p.i)

Fig. 2

Reactome functional interaction network corresponding to 148 genes that show differential expression in the T0 (fasting) vs T1 (5 h after eating) comparison. Nodes in different network modules are displayed in different colors. Letters in parentheses represent the source database as follows: R – Reactome, K – KEGG, and B – BioCarta. Enriched pathways (q-value <0.05) in each one of the individual network modules are: 1: Proteoglycans in cancer (K); 2: TNF signaling (R); 3: Circadian clock (R); 4: Bone remodeling (B); 5: Striated muscle contraction (R) and 6: Transcriptional regulation of pluripotent stem cells (R)

Fig. 3

Reactome functional interaction network corresponding to 520 genes showing differential expression in the T0 (fasting) vs T2 (7 h after eating) comparisons. Nodes in different network modules are displayed in different colors. Letters in parentheses represent the source database as follows: R – Reactome, K – KEGG, N – NCI PID, P - Panther, and B – BioCarta. Enriched pathways (q-value <0.05) in each one of the individual network modules are: 1: Mitotic G1-G1/S phases (R); 2: Nicotinic acetylcholine receptor signaling pathway (P); 3: SRP-dependent co-translational protein targeting to membrane (R); 4: Senescence-associated secretory phenotype (SASP) (R); 5: Signaling events mediated by HDAC Class II (N); 6: Circadian rhythm pathway (N), 7: Oxidative stress induced gene expression via Nrf2 (B); 8: ABC-family proteins mediated transport (R); 9: Toll-like receptors cascades (R); 11: Proximal tubule bicarbonate reclamation (K); 12: Wnt signaling pathway (K); 13: Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways (R); 14: ATF-2 transcription factor network (N); 15: ECM-receptor interaction (K); 16: GPCR ligand binding (R); 17: Oxidative phosphorylation (K); 18: Integrin signalling pathway (P); 19: Myogenesis (R); 20: Transcriptional regulation of white adipocyte differentiation (R)

Fig. 4

Reactome functional interaction network corresponding to 135 genes showing differential expression in the T1 (5 h after eating) vs T2 (7 h after eating) comparison. Nodes in different network modules are displayed in different colors. Letters in parentheses represent the source database as follows: R – Reactome and K – KEGG. Enriched pathways (q-value <0.05) in each one of the individual network modules are: 1: SRP-dependent cotranslational protein targeting to membrane (R); 2: Eukaryotic Translation Termination (R); 3: Oxidative phosphorylation (K) and 4: Parkinson’s disease (K)