Gong Yan, Zhang Yuebo, Li Biao, Xiao Yu, Zeng Qinghua, Xu Kang, Duan Yehui, He Jianhua, Ma Haiming
College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China.
Ningxiang Pig Farm of Dalong Livestock Technology Co. Ltd., Ningxiang 410600, China.
Biology (Basel). 2021 Apr 8;10(4):310. doi: 10.3390/biology10040310.
Ningxiang pigs, a fat-type pig, are native to Ningxiang County in Hunan Province, with thousands of years of breeding history. This study aims to explore the expression profiles and functional networks on messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) in the liver. Liver tissue of Ningxiang piglets was collected at 30, 90, 150, and 210 days after birth (four development stages), and the mRNA and lncRNA expression was profiled. Compared to mRNA and lncRNA expression profiles, most differentially expressed mRNAs (DEmRNAs) were upregulated at 30 days; however, most DElncRNAs were downregulated at 210 days. Via Short Time-series Expression Miner (STEM) analysis and weighted gene co-expression network analysis (WGCNA), a complex interaction between mRNAs and lncRNAs was identified, indicating that lncRNAs may be a critical regulatory element for mRNAs. One module of genes in particular (module profile 4) was related to fibril organization, vasculogenesis, GTPase activator activity, and regulation of kinase activity. The mRNAs and lncRNAs in module profile 4 had a similar pattern of expression, indicating that they have functional and regulatory relationships. Only , , and in the particular mRNA profile 4 were the target genes of lncRNAs in that profile, which shows the possible regulatory relationship between lncRNAs and mRNAs. The expression of these genes and lncRNAs in profile 4 was the highest at 30 days, and it is believed that these RNAs may play a critical role during the suckling period in order to meet the dietary requirements of piglets. In the lncRNA-mRNA co-expression network, the identified gene hubs and associated lncRNAs were shown to be involved in saccharide, lipid, and glucose metabolism, which may play an important role in the development and health of the liver. This result will lead to further investigation of liver lncRNA functions at various stages of development in Ningxiang pigs.
宁乡猪是一种脂肪型猪，原产于湖南省宁乡县，有着数千年的养殖历史。本研究旨在探究肝脏中信使核糖核酸（mRNA）和长链非编码核糖核酸（lncRNA）的表达谱及功能网络。在出生后30、90、150和210天（四个发育阶段）采集宁乡仔猪的肝脏组织，并对mRNA和lncRNA表达进行分析。与mRNA和lncRNA表达谱相比，大多数差异表达的mRNA（DEmRNA）在30天时上调；然而，大多数差异表达的lncRNA（DElncRNA）在210天时下调。通过短时序列表达挖掘工具（STEM）分析和加权基因共表达网络分析（WGCNA），确定了mRNA和lncRNA之间的复杂相互作用，表明lncRNA可能是mRNA的关键调控元件。特别是一个基因模块（模块谱4）与纤维组织形成、血管生成、GTP酶激活活性及激酶活性调节有关。模块谱4中的mRNA和lncRNA具有相似的表达模式，表明它们具有功能和调控关系。在特定的mRNA谱4中，只有、和是该谱中lncRNA的靶基因，这显示了lncRNA与mRNA之间可能的调控关系。这些基因和lncRNA在谱4中的表达在30天时最高，据信这些RNA可能在哺乳期发挥关键作用，以满足仔猪的饮食需求。在lncRNA-mRNA共表达网络中，鉴定出的基因枢纽和相关lncRNA参与了糖类、脂质和葡萄糖代谢，这可能对肝脏的发育和健康起重要作用。这一结果将促使对宁乡猪肝脏lncRNA在不同发育阶段的功能进行进一步研究。
