Transcriptome analysis of miRNA and mRNA in the livers of pigs with highly diverged backfat thickness

Kai Xing,Hong Ao,Yuan Wang,Yong Guo,Fengxia Zhang,Chuduan Wang,Yibing Liu,Hemin Ni,Ting Yang,Zhen Tan,Xitong Zhao,Shaokang Chen,Zhuocheng Hou

doi:10.1038/s41598-019-53377-x

Abstract

Fat deposition is very important in pig production, and its mechanism is not clearly understood. MicroRNAs (miRNAs) play critical roles in fat deposition and energy metabolism. In the current study, we investigated the mRNA and miRNA transcriptome in the livers of Landrace pigs with extreme backfat thickness to explore miRNA-mRNA regulatory networks related to lipid deposition and metabolism. A comparative analysis of liver mRNA and miRNA transcriptomes from pigs (four pigs per group) with extreme backfat thickness was performed. We identified differentially expressed genes from RNA-seq data using a Cufflinks pipeline. Seventy-one differentially expressed genes (DEGs), including twenty-eight well annotated on the porcine reference genome genes, were found. The upregulation genes in pigs with higher backfat thickness were mainly involved in fatty acid synthesis, and included fatty acid synthase (FASN), glucokinase (GCK), phosphoglycerate dehydrogenase (PHGDH), and apolipoprotein A4 (APOA4). Cytochrome P450, family 2, subfamily J, polypeptide 34 (CYP2J34) was lower expressed in pigs with high backfat thickness, and is involved in the oxidation of arachidonic acid. Moreover, 13 differentially expressed miRNAs were identified. Seven miRNAs were associated with fatty acid synthesis, lipid metabolism, and adipogenic differentiation. Based on comprehensive analysis of the transcriptome of both mRNAs and miRNAs, an important regulatory network, in which six DEGs could be regulated by differentially expressed miRNAs, was established for fat deposition. The negative correlate in the regulatory network including, miR-545-5p and GRAMD3, miR-338 and FASN, and miR-127, miR-146b, miR-34c, miR-144 and THBS1 indicate that direct suppressive regulation may be involved in lipid deposition and energy metabolism. Based on liver mRNA and miRNA transcriptomes from pigs with extreme backfat thickness, we identified 28 differentially expressed genes and 13 differentially expressed miRNAs, and established an important miRNA-mRNA regulatory network. This study provides new insights into the molecular mechanisms that determine fat deposition in pigs.

Highlights

MiRNAs are a group of small non-coding RNAs, which are present in all metazoans and play key roles in diverse biological processes and metabolism[1,2]
We identified 28 genes and 13 miRNAs that were differentially expressed in the livers of Landrace pigs with extreme and divergent backfat thickness in this population
A few miRNAs that target genes involved in fatty acid synthesis, lipid metabolism, and adipogenic differentiation were found to be differentially expressed

Summary

Introduction

MiRNAs are a group of small (approximately 22 nucleotide) non-coding RNAs, which are present in all metazoans and play key roles in diverse biological processes and metabolism[1,2]. MiRNAs have been reported to play important roles in the regulation of fat deposition and energy metabolism. Levels of fatness and leanness are very important in pig production because of their ability to affect productive performance, meat quality, and reproductive performance[12,13]. Due to their anatomical, physiological, and genetic similarities to humans, and their high level of fat deposition, pigs represent a suitable model for use in the study of human obesity and energy metabolism[14]. Liver is suitable tissue to study the molecular mechanisms of fat deposition and metabolism in pigs

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Discussion

Conclusion