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Circular RNA expression profiles in the porcine liver of two distinct phenotype pig breeds.

ABSTRACT: OBJECTIVE:An experiment was conducted to identify and characterize the circular RNA expression and metabolic characteristics in the liver of Jinhua pigs and Landrace pigs. METHODS:Three Jinhua pigs and three Landrace pigs respectively at 70-day were slaughtered to collect the liver tissue samples. Immediately after slaughter, blood samples were taken to detect serum biochemical indicators. Total RNA extracted from liver tissue samples were used to prepare the library and then sequence on HiSeq 2500. Bioinformatic methods were employed to analyze sequence data to identify the circRNAs and predict the potential roles of differentially expressed circRNAs between the two breeds. RESULTS:Significant differences in physiological and biochemical traits were observed between growing Jinhua and Landrace pigs. We identified 84,864 circRNA candidates in two breeds and 366 circRNAs were detected as significantly differentially expressed. Their host genes are involved in lipid biosynthetic and metabolic processes according to the gene ontology analysis and associated with metabolic pathways. CONCLUSION:Our research represents the first description of circRNA profiles in the porcine liver from two divergent phenotype pigs. The predicted miRNA-circRNA interaction provides important basis for miRNA-circRNA relationships in the porcine liver. These data expand the repertories of porcine circRNA and are conducive to understanding the possible molecular mechanisms involved in miRNA and circRNA. Our study provides basic data for further research of the biological functions of circRNAs in the porcine liver.

SUBMITTER: Huang M

PROVIDER: S-EPMC5933978 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundMycoplasma hyopneumoniae (Mhp) is the main pathogen causing respiratory disease in the swine industry. Mhp infection rates differ across pig breeds, with Chinese native pig breeds that exhibit high fecundity (e.g., Jiangquhai, Meishan, Erhualian) more sensitive than Duroc, Landrace, and other imported pig breeds. However, the genetic basis of the immune response to Mhp infection in different pig breeds is largely unknown.AimsThe aims of this study were to determine the relative Mhp susceptibility of the Chinese native Jiangquhai breed compared to the Duroc breed, and identify molecular mechanisms of differentially expressed genes (DEGs) using an RNA-sequencing (RNA-seq) approach.MethodsJiangquhai and Duroc pigs were artificially infected with the same Mhp dose. The entire experiment lasted 28 days. Daily weight gain, Mhp-specific antibody levels, and lung lesion scores were measured to evaluate the Mhp infection susceptibility of different breeds. Experimental pigs were slaughtered on the 28th day. Lung tissues were collected for total RNA extraction. RNA-seq was performed to identify DEGs, which were enriched by gene ontology (GO) and the Kyoto Encyclopedia annotation of Genes and Genomes (KEGG) databases. DEGs were validated with real-time quantitative polymerase chain reaction (RT-qPCR).ResultsInfection with the same Mhp dose produced a more serious condition in Jiangquhai pigs than in Duroc pigs. Jiangquhai pigs showed poorer growth, higher Mhp antibody levels, and more serious lung lesions compared with Duroc pigs. RNA-seq identified 2,250 and 3,526 DEGs in lung tissue from Jiangquhai and Duroc pigs, respectively. The two breeds shared 1,669 DEGs, which were involved in immune-relevant pathways including cytokine-cytokine receptor interaction, PI3K-Akt signaling pathway, and chemokine signaling pathway. Compared to Jiangquhai pigs, more chemokines, interferon response factors, and interleukins were specifically activated in Duroc pigs; CXCL10, CCL4, IL6 and IFNG genes were significantly up-regulated, which may help Duroc pigs enhance immune response and reduce Mhp susceptibility.ConclusionThis study demonstrated differential immune-related DEGs in lung tissue from the two breeds, and revealed an important role of genetics in the immune response to Mhp infection. The biological functions of these important DEGs should be further confirmed and maybe applied as molecular markers that improve pig health.

Project description:The liver is a complex organ governing several physiological processes that define biological mechanisms affecting growth, feed efficiency and performance traits in all livestock species, including pig. Proteomics may contribute to a better understanding of the relationship between liver functions and complex production traits in pigs and to characterize this species as biomedical model. This study applied, for the first time, a label-free liquid chromatography-mass spectrometry (LC-MS) proteomic approach to compare the liver proteome profiles of two important heavy pig breeds, Italian Duroc and Italian Large White. Liver specimens were collected (after slaughtering) from performance tested pigs of these two breeds, raised in standard conditions. The label-free LC-MS method captured a total of 501 proteins of which 200 were subsequently considered in the between breeds comparison. A statistical pipeline based on the sparse Partial Least Squares Discriminant Analysis (sPLS-DA), coupled with stability and significance tests, was applied for the identification of up or down regulated proteins between breeds. This analysis revealed a total of 25 proteins clearly separating Italian Duroc and Italian Large White pigs. Among the top proteins differentiating the two breeds, 3-ketoacyl-CoA thiolase, mitochondrial (ACAA2) and histone H2B type 2-F (HIST2H2BF) were up-regulated in Italian Duroc pigs and carboxylesterase 3 (CES3) and ketohexokinase (KHK) were up-regulated in Italian Large White pigs. Fatty acid synthase (FASN), involved in fatty acid metabolism and encoded by a gene located in a QTL region for fatty acid composition, was up-regulated in Italian Large White pigs. The in silico protein interaction analysis showed that 16 of these proteins were connected in one big module. Bioinformatic functional analysis indicated that differentially expressed proteins were involved in several biological processes related to the metabolism of lipids, amino-acids, carbohydrates, cofactors and antibiotics/drugs, suggesting that these functions might distinguish Italian Duroc and Italian Large White pigs. This pilot comparative proteomic analysis of the porcine liver highlighted several biological factors that could determine the peculiar production potentials of these two heavy pig breeds, derived by their different genetic backgrounds.

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Circular RNA expression profiles in the porcine liver of two distinct phenotype pig breeds.

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