RNA-Seq Analysis of the Key Long Noncoding RNAs and mRNAs Related to the Regulation of Hepatic Lipid Metabolism in Oreochromis niloticus
RNA-Seq Analysis of the Key Long Noncoding RNAs and mRNAs Related to the Regulation of Hepatic Lipid Metabolism in Oreochromis niloticus
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DOI：
10.3390/fishes7060332
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发表时间：
2022-11
期刊：
影响因子：
2.3
通讯作者：
Yifan Tao;Siqi Lu;Tao Zheng;Mingxiao Li;J. Qiang;P. Xu
中科院分区：
文献类型：
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作者：
Yifan Tao;Siqi Lu;Tao Zheng;Mingxiao Li;J. Qiang;P. Xu
遗传改良养殖罗非鱼（Oreochromis niloticus，GIFT）在集约化养殖过程中容易发生肝脏代谢失衡和脂肪肝疾病。长链非编码RNA（lncRNA）在包括脂质代谢在内的多种生物学过程中发挥重要作用。然而，参与罗非鱼肝脏脂质代谢的lncRNA尚未被鉴定。在这项研究中，对喂食高脂肪饮食（HFD，18.5%脂质）或正常脂肪饮食（NFD，8%脂质）56天的幼年雄性GIFT的肝脏进行了Illumina测序和生物信息学分析。RNA-seq分析揭示了这两组之间的299个差异表达（DE）-mRNA和284个DE-lncRNA。通过qRT-PCR验证了14个候选物（7个DE-mRNA和7个DE-lncRNA）的转录谱，结果与RNA-seq结果一致。预测了DE-lncRNA的65个顺式靶基因和3610个反式靶基因。功能分析表明，多种代谢途径受到高脂肪摄入的影响，包括过氧化物酶体增殖物激活受体信号通路，脂肪酸降解和脂肪酸代谢途径。共表达网络分析表明，许多lncRNA与许多参与脂质代谢的基因相互作用，并且一些基因受到多个lncRNA的调控。研究了三种lncRNA（MSTRG.14598.1、MSTRG.6725.3和MSTRG.13364.2）及其在PPAR信号传导途径中的潜在靶基因（faldh、slc 25 a48和fabp 7a）的表达模式。我们的研究为罗非鱼脂质代谢相关lncRNA的研究提供了新的信息。
Genetically improved farmed tilapia (Oreochromis niloticus, GIFT) is prone to hepatic metabolic imbalances and fatty liver disease during intensive farming. Long non-coding RNAs (lncRNAs) perform essential roles in various biological processes, including lipid metabolism. However, the lncRNAs involved in hepatic lipid metabolism in tilapia have not yet been identified. In this study, Illumina sequencing and bioinformatic analyses were performed on the liver of juvenile male GIFT fed a high-fat diet (HFD, 18.5% lipid) or a normal-fat diet (NFD, 8% lipid) for 56 days. RNA-seq analyses revealed 299 differentially expressed (DE)-mRNAs and 284 DE-lncRNAs between these two groups. The transcript profiles of 14 candidates (seven DE-mRNA and seven DE-lncRNAs) were verified by qRT-PCR, and the results were consistent with the RNA-seq results. Furthermore, 65 cis target genes and 3610 trans target genes of DE-lncRNAs were predicted. Functional analyses suggested that multiple metabolic pathways are affected by a high fat intake, including the PPAR signaling, fatty acid degradation, and fatty acid metabolism pathways. A co-expression network analysis indicated that many lncRNAs interact with numerous genes involved in lipid metabolism, and that some genes are regulated by multiple lncRNAs. The expression patterns of three lncRNAs (MSTRG.14598.1, MSTRG.6725.3, and MSTRG.13364.2) and their potential target genes (faldh, slc25a48, and fabp7a) in the PPAR signaling pathway were investigated. Our study provides new information about lncRNAs associated with lipid metabolism in tilapia.