Li Hong, Gu Zhenzhen, Yang Liyu, Tian Yadong, Kang Xiangtao, Liu Xiaojun
College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China.
Cell Physiol Biochem. 2018;50(5):1638-1658. doi: 10.1159/000494785. Epub 2018 Nov 1.
BACKGROUND/AIMS: Accumulating evidences have demonstrated that long noncoding RNAs (lncRNA) play important roles in hepatic lipid metabolism in mammals. However, no systematic screening of the potential lncRNAs in the livers of laying hens has been performed, and few studies have been reported concerning the effects of the lncRNAs on lipid metabolism in the livers of chickens during egg-laying period. The purpose of this study was to compare the difference in lncRNA expression in the livers of pre-laying and peak-laying hens at the age of 20 and 30 weeks old by transcriptome sequencing and to investigate the interaction networks among lncRNAs, mRNAs and miRNAs. Moreover, the regulatory mechanism and biological function of lncLTR, a significantly differentially expressed lncRNA in the liver between pre- and peak-laying hens, was explored in vitro and in vivo.
Bioinformatics analyses were conducted to identify the differentially expressed (DE) lncRNAs between the two groups of hens. The target genes of the DE lncRNA were predicated for further functional enrichment. An integrated analysis was performed among the DE lncRNA datasets, DE mRNAs and DE miRNA datasets obtained from the same samples to predict the interaction relationship. In addition, in vivo and in vitro trials were carried out to determine the expression regulation of lncLTR, and polymorphism association analysis was conducted to detect the biological role of ncLTR.
A total of 124 DE lncRNAs with a P-value ≤ 0.05 were identified. Among them, 44 lncRNAs including 30 known and 14 novel lncRNAs were significant differentially expressed (SDE) with FDR ≤ 0.05. Thirty-two lncRNAs were upregulated and 12 were downregulated in peak-laying group compared with pre-laying group. The functional enrichment results revealed that target genes of some lncRNAs are involved in the lipid metabolism process. Integrated analysis suggested that some of the genes involved in lipid metabolism might be regulated by both the lncRNA and the miRNA. In addition, an upregulated lncRNA, designated lncLTR, was demonstrated to be induced by estrogen via ERβ signaling. The c242. G>A SNP in lncLTR was significantly associated with chicken carcass weight, evisceration weight, semi-evisceration weight, head weight, double-wing weight, claw weight traits, and blood biochemical index, especially for the blood triglyceride content.
A series of lncRNAs associated with lipid metabolism in the livers of chickens were identified by transcriptome sequencing and functional analysis, providing a valuable data resource for further studies on chicken hepatic metabolism activities. LncLTR was regulated by estrogen via ERβ signaling and associated with chicken carcass trait and blood triglyceride content.
背景/目的：越来越多的证据表明，长链非编码RNA（lncRNA）在哺乳动物肝脏脂质代谢中发挥重要作用。然而，尚未对蛋鸡肝脏中潜在的lncRNA进行系统筛选，关于lncRNA对产蛋期鸡肝脏脂质代谢影响的研究报道较少。本研究旨在通过转录组测序比较20周龄和30周龄产蛋前和产蛋高峰期母鸡肝脏中lncRNA表达的差异，并研究lncRNA、mRNA和miRNA之间的相互作用网络。此外，还在体外和体内探索了产蛋前和产蛋高峰期母鸡肝脏中显著差异表达的lncRNA——lncLTR的调控机制和生物学功能。
进行生物信息学分析以鉴定两组母鸡之间差异表达的（DE）lncRNA。对DE lncRNA的靶基因进行预测以进行进一步的功能富集。对从同一样本获得的DE lncRNA数据集、DE mRNA和DE miRNA数据集进行综合分析，以预测相互作用关系。此外，进行体内和体外试验以确定lncLTR的表达调控，并进行多态性关联分析以检测ncLTR的生物学作用。
共鉴定出124个P值≤0.05的DE lncRNA。其中，44个lncRNA（包括30个已知lncRNA和14个新lncRNA）差异显著（SDE），FDR≤0.05。与产蛋前组相比，产蛋高峰期组中有32个lncRNA上调，12个lncRNA下调。功能富集结果表明，一些lncRNA的靶基因参与脂质代谢过程。综合分析表明，一些参与脂质代谢的基因可能受lncRNA和miRNA共同调控。此外，一个上调的lncRNA，命名为lncLTR，被证明可通过雌激素受体β（ERβ）信号通路被雌激素诱导。lncLTR中的c242.G>A单核苷酸多态性（SNP）与鸡的胴体重、屠体重、半净膛重、头重、双翅重、爪重性状以及血液生化指标显著相关，尤其是血液甘油三酯含量。
通过转录组测序和功能分析鉴定出一系列与鸡肝脏脂质代谢相关的lncRNA，为进一步研究鸡肝脏代谢活动提供了有价值的数据资源。lncLTR受雌激素通过ERβ信号通路调控，并与鸡的胴体性状和血液甘油三酯含量相关。
