Coordinated miRNA/mRNA Expression Profiles for Understanding Breed-Specific Metabolic Characters of Liver between Erhualian and Large White Pigs

Abstract

MicroRNAs (miRNAs) are involved in the regulation of various metabolic processes in the liver, yet little is known on the breed-specific expression profiles of miRNAs in coordination with those of mRNAs. Here we used two breeds of male newborn piglets with distinct metabolic characteristics, Large White (LW) and Erhualian (EHL), to delineate the hepatic expression profiles of mRNA with microarray and miRNAs with both deep sequencing and microarray, and to analyze the functional relevance of integrated miRNA and mRNA expression in relation to the physiological and biochemical parameters. EHL had significantly lower body weight and liver weight at birth, but showed elevated serum levels of total cholesterol (TCH), high-density lipoprotein cholesterol (HDLC) and low-density lipoprotein cholesterol (LDLC), as well as higher liver content of cholesterol. Higher serum cortisol and lower serum insulin and leptin were also observed in EHL piglets. Compared to LW, 30 up-regulated and 18 down-regulated miRNAs were identified in the liver of EHL, together with 298 up-regulated and 510 down-regulated mRNAs (FDR<10%). RT-PCR validation of some differentially expressed miRNAs (DEMs) further confirmed the high-throughput data analysis. Using a target prediction algorithm, we found significant correlation between the up-regulated miRNAs and down-regulated mRNAs. Moreover, differentially expressed genes (DEGs), which are involved in proteolysis, were predicted to be mediated by DEMs. These findings provide new information on the miRNA and mRNA profiles in porcine liver, which would shed light on the molecular mechanisms underlying the breed-specific traits in the pig, and may serve as a basis for further investigation into the biological functions of miRNAs in porcine liver.

Global correlation analysis for microRNA and gene expression profiles in human obesity

“…We conducted further examinations on the DEG numbers in the target genes of DEMs using Fisher's exact test to determine whether the number of predicted target genes of DEMs that were differentially regulated was higher than would be expected was by chance [23]. P values less than 0.05 were set as the threshold.…”

Identification and bioinformatics analysis of microRNAs associated with stress and immune response in serum of heat-stressed and normal Holstein cows

“…However, such approaches were limited in their ability to detect rare miRNAs, or tissue-specific miRNAs from tissues that are difficult to obtain. In mammals, temporal and spatial changes in miRNA expression have been well characterized to delineate the miRNA transcription of different tissues at different developmental stages (Li et al 2010) or in different species (Li et al 2012). At the same time, one study clearly demonstrated that levels of miRNAs in serum are stable, reproducible, and consistent among individuals of the same animal species .…”

Glucocorticoid receptor is involved in the breed-dependent transcriptional regulation of mtDNA- and nuclear-encoded mitochondria genes in the liver of newborn piglets

“…Previous studies indicate striking breed differences in hepatic metabolism in the pig [5,31]. Although it is well known that hepatic metabolism is closely related to mitochondrial functions, no direct evidence of breed differences in mitochondrial function is available in the pig.…”

“…Numerous studies have been undertaken to reveal the genetic and physiological mechanisms underlying the striking breed differences [2,3]. The disparity in the regulation of energy homeostasis appears to be the main attribute for the various breed-specific traits [4,5]. …”

“…Hepatocytes contain a large number of mitochondria which play an important role in the energy homeostasis [7]. We identified, by comparing the hepatic transcriptome of LW and EHL piglets, that mitochondrial related genes consist of 5% (48/808) of all the differentially expressed genes [5]. Among these mitochondrial related genes, isocitrate dehydrogenase 2 ( IDH2 ), adenylate kinase 1 ( AK1 ) and ATP synthase, H + transporting, mitochondrial Fo complex, subunit d ( ATP5H ) are nuclear-encoded and closely related to cellular ATP content.…”