Identification of Differentially Expressed MicroRNAs and Their Potential Target Genes in Adipose Tissue from Pigs with Highly Divergent Backfat Thickness.

Kai Xing,Chuduan Wang,Yong Guo,Xihui Sheng,Yibing Liu,Fengxia Zhang,Zhen Tan,Xiaolong Qi,Hemin Ni,Xitong Zhao,Xiangguo Wang

doi:10.3390/ani10040624

Abstract

Simple SummaryThe role of microRNA in fat deposition is very important and not clearly understood. We detected 318 pig microRNAs (miRNAs), among high and low backfat tissue samples, by high throughput sequencing. Among them, 18 miRNAs were differentially expressed between the high and low backfat groups. Some of the differentially expressed miRNAs were involved mainly in lipid and carbohydrate metabolism, and glycan biosynthesis and metabolism. In addition, in silico analysis of the mRNA and miRNA transcriptomes, revealed possible regulatory relationships for fat deposition. In particular, three miRNA–mRNA pairs, miR-137–PPARGC1A, miR-141–FASN, and miR-122-5p–PKM, were identified as candidate key regulators of fat deposition. Our findings provide an important insight into miRNA expression patterns in backfat tissue of pig and new insights into the regulatory mechanisms of fat deposition in pig.Fatty traits are very important in pig production. However, the role of microRNAs (miRNAs) in fat deposition is not clearly understood. In this study, we compared adipose miRNAs from three full-sibling pairs of female Landrace pigs, with high and low backfat thickness, to investigate the associated regulatory network. We obtained an average of 17.29 million raw reads from six libraries, 62.27% of which mapped to the pig reference genome. A total of 318 pig miRNAs were detected among the samples. Among them, 18 miRNAs were differentially expressed (p-value < 0.05, |log2fold change| ≥ 1) between the high and low backfat groups; 6 were up-regulated and 12 were down-regulated. Functional enrichment of the predicted target genes of the differentially expressed miRNAs, indicated that these miRNAs were involved mainly in lipid and carbohydrate metabolism, and glycan biosynthesis and metabolism. Comprehensive analysis of the mRNA and miRNA transcriptomes revealed possible regulatory relationships for fat deposition. Negatively correlated mRNA–miRNA pairs included miR-137–PPARGC1A, miR-141–FASN, and miR-122-5p–PKM, indicating these interactions may be key regulators of fat deposition. Our findings provide important insights into miRNA expression patterns in the backfat tissue of pig and new insights into the regulatory mechanisms of fat deposition in pig.

Highlights

Pig (Sus scrofa) is a vital agricultural animal for meat production [1]
These results indicated that the Differentially expressed miRNAs (DEMs) identified using the RNA sequencing (RNA-seq) data were were reliable
Significant in backfat thickness, no differences in body weight, were±observed the pigsdifferences in the high backfat (HB) and low backfat (LB) groups, whichbut implied that the differences in fat were observed between the pigs in the groups, which implied that the differences in fat deposition were not caused by changes in body weight

Summary

Introduction

Fat deposition is an important economic trait because it is correlated with carcass quality, meat quality, and consumer palatability [2]. Backfat thickness is a good indicator for fat deposition, and is usually measured within a certain period and at a specific age, adjusted to a specified weight (100 kg). Selection for reduced backfat thickness has been effective [4] and is used directly in pig breeding [5]. MicroRNAs (miRNAs) are 18–22 base pair (bp) non-coding RNAs that are thought to regulate more than 60% of genes in almost all physiological and pathological processes [6]. Fat deposition is a complex biological process regulated by multiple factors, including miRNAs. In adipose tissue, miRNAs have been found to play important roles in adipocyte differentiation [7] and lipid metabolism [8]. MiR-127 was found to be a negative regulator of adipogenesis by targeting the genes encoding mitogen-activated protein kinase 4 (MKK4) and homeobox C6 (HOXC6) in porcine adipocytes [9], and miR-302a inhibited adipogenesis by interacting with the 30 UTR of peroxisome proliferator activated receptor gamma (PPARγ) mRNA [10]

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Conclusion