Co-expression network analysis predicts a key role of microRNAs in the adaptation of the porcine skeletal muscle to nutrient supply

Abstract

Background: The role of non-coding RNAs in the porcine muscle metabolism is poorly understood, with few studies investigating their expression patterns in response to nutrient supply. Therefore, we aimed to investigate the changes in microRNAs (miRNAs), long intergenic non-coding RNAs (lincRNAs) and mRNAs muscle expression before and after food intake. Results: We measured the miRNA, lincRNA and mRNA expression levels in the gluteus medius muscle of 12 gilts in a fasting condition (AL-T0) and 24 gilts fed ad libitum during either 5 h. (AL-T1, N = 12) or 7 h. (AL-T2, N = 12) prior to slaughter. The small RNA fraction was extracted from muscle samples retrieved from the 36 gilts and sequenced, whereas lincRNA and mRNA expression data were already available. In terms of mean and variance, the expression profiles of miRNAs and lincRNAs in the porcine muscle were quite different than those of mRNAs. Food intake induced the differential expression of 149 (AL-T0/AL-T1) and 435 (AL-T0/AL-T2) mRNAs, 6 (AL-T0/AL-T1) and 28 (AL-T0/AL-T2) miRNAs and none lincRNAs, while the number of differentially dispersed genes was much lower. Among the set of differentially expressed miRNAs, we identified ssc-miR-148a-3p, ssc-miR-22-3p and ssc-miR-1, which play key roles in the regulation of glucose and lipid metabolism. Besides, co-expression network analyses revealed several miRNAs that putatively interact with mRNAs playing key metabolic roles and that also showed differential expression before and after feeding. One case example was represented by seven miRNAs (ssc-miR-148a-3p, ssc-miR-151-3p, ssc-miR-30a-3p, ssc-miR-30e-3p, ssc-miR-421-5p, ssc-miR-493-5p and ssc-miR-503) which putatively interact with the PDK4 mRNA, one of the master regulators of glucose utilization and fatty acid oxidation. Conclusions: As a whole, our results evidence that microRNAs are likely to play an important role in the porcine skeletal muscle metabolic adaptation to nutrient availability.

Modeling microRNA-driven post-transcriptional regulation by using exon-intron split analysis (EISA) in pigs

“…Expression data and experimental conditions employed to infer gene covariation networks and regulatory connections were previously described in [19][20][21].…”

“…RNA extraction, RNA-Seq and small RNA-Seq sequencing protocols, quality-check preprocessing and mapping were performed as previously described [19][20][21]. In brief, total RNA was isolated from GM tissue using the RiboPure kit (Ambion, Austin, TX) and following the manufacturer's recommendations, while for RNA from adipocytes, the protocol from Cirera et al 2013 [26] specifically adapted to adipose tissue was implemented.…”

MicroRNAs as Biomarkers for Animal Health and Welfare in Livestock

“…Heat stress also influences muscle development, modifying the balance between protein synthesis and degradation (149). Several studies have investigated the role of miRNAs in muscle development under different environmental conditions and in different breeds (150)(151)(152)(153)(154). Hao et al investigated for the first time how heat stress affected the muscle miRNA expression profile of cross-bred barrows (155).…”

Integrated Genome-Wide Analysis of MicroRNA Expression Quantitative Trait Loci in Pig Longissimus Dorsi Muscle

“…Several miRNAs expressed specifically in muscle tissue have been termed the “myomiRs” (miR-1, miR-133a, miR-133b, miR-206, and others), which play critical roles in the proliferation, differentiation, and regeneration of skeletal muscle (for review, see Horak et al, 2016 ). Previous studies demonstrate miRNA involvement in skeletal muscle development and function in pigs, spanning various developmental time points, physiological states, and breeds ( Qin et al, 2013 ; Siengdee et al, 2013 ; Cai et al, 2015 ; Jing et al, 2015 ; Mai et al, 2016 ; Xi et al, 2018 ; Mármol-Sánchez et al, 2020 ). While many studies have examined effects of miRNAs on diverse phenotypes in pigs, less has been done to elucidate mechanisms regulating the expression of miRNAs themselves, and their effects on downstream phenotypes.…”