Key Laboratory of Animal Physiology & Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China.
PLoS One. 2012;7(6):e38716. doi: 10.1371/journal.pone.0038716. Epub 2012 Jun 12.
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.
微小 RNA（miRNA）参与肝脏中各种代谢过程的调控，但关于 miRNA 与 mRNA 的协调表达谱在品种特异性方面的信息知之甚少。本研究使用两种具有不同代谢特征的雄性新生仔猪品种（大白猪[LW]和二花脸猪[EHL]），通过微阵列描绘 mRNA 的肝脏表达谱、深度测序和微阵列描绘 miRNA 的表达谱，并分析整合的 miRNA 和 mRNA 表达与生理和生化参数之间的功能相关性。EHL 仔猪在出生时体重和肝脏重量显著较低，但血清总胆固醇（TCH）、高密度脂蛋白胆固醇（HDLC）和低密度脂蛋白胆固醇（LDLC）水平升高，胆固醇肝脏含量也较高。EHL 仔猪的血清皮质醇水平较高，而血清胰岛素和瘦素水平较低。与 LW 相比，EHL 肝脏中有 30 个上调和 18 个下调的 miRNA，以及 298 个上调和 510 个下调的 mRNA（FDR<10%）。一些差异表达 miRNA（DEM）的 RT-PCR 验证进一步证实了高通量数据分析。使用靶标预测算法，我们发现上调的 miRNA 与下调的 mRNAs 之间存在显著相关性。此外，参与蛋白水解的差异表达基因（DEGs）被预测由 DEMs 介导。这些发现为猪肝脏中的 miRNA 和 mRNA 谱提供了新的信息，这将有助于阐明猪品种特异性特征的分子机制，并可能为进一步研究 miRNA 在猪肝脏中的生物学功能提供基础。
