Identification and Characterization of Long Non-coding RNAs in the Intestine of Olive Flounder (Paralichthys olivaceus) During Edwardsiella tarda Infection.
Identification and Characterization of Long Non-coding RNAs in the Intestine of Olive Flounder (Paralichthys olivaceus) During Edwardsiella tarda Infection.
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DOI：
10.3389/fimmu.2021.623764
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发表时间：
2021
影响因子：
7.3
通讯作者：
Li C
中科院分区：
文献类型：
--
作者：
Xiu Y;Li Y;Liu X;Su L;Zhou S;Li C
长链非编码RNA（lncRNA）在包括免疫应答在内的基本生物学过程中发挥着广泛的作用。橄榄比目鱼（Paralichthys olivaceus）是日本、韩国和中国广泛养殖的重要经济比目鱼，受到细菌、病毒和寄生虫等传染性病原体的威胁。然而，lncRNA在该物种对病原体感染的免疫应答中的作用尚不清楚。因此，在本研究中，我们的目的是确定lncRNA在肠道中的橄榄比目鱼和评估其差异表达谱在迟缓爱德华氏菌感染，这是一个重要的人畜共患病和肠道病原体。共鉴定了4,445个推定的lncRNA，包括3,975个新的lncRNA和470个注释的lncRNA。这些lncRNA与mRNA相比具有较短的长度和较少的外显子。共鉴定出115个差异表达的lncRNA（DE-lncRNA）。迟发性感染为了验证lncRNA的表达模式，随机选择六个DE-lncRNA用于定量实时PCR。预测DE-lncRNA的共定位和共表达的mRNA，用于进行基因本体论（GO）和京都基因和基因组百科全书（KEGG）富集分析。DE-lncRNA的靶基因丰富了许多免疫相关的过程，并表现出与免疫相关的信号通路的强相关性。为了更好地了解lncRNA的广泛调控功能，构建了lncRNA-miRNA-mRNA调控网络，并首次从油鲽肠道中初步鉴定了两个潜在的竞争性内源RNA（ceRNA）网络LNC_001979-novel_171-Potusc 2和LNC_001979-novel_171-Podad 1。总之，本研究提供了一个宝贵的注释和lncRNA表达谱在橄榄比目鱼感染E。这为进一步研究lncRNA在比目鱼肠粘膜免疫应答中的调控功能奠定了基础。
Long non-coding RNAs (lncRNAs) play widespread roles in fundamental biological processes, including immune responses. The olive flounder (Paralichthys olivaceus), an important economical flatfish widely cultured in Japan, Korea, and China, is threatened by infectious pathogens, including bacteria, viruses, and parasites. However, the role of lncRNAs in the immune responses of this species against pathogen infections is not well-understood. Therefore, in this study, we aimed to identify lncRNAs in the intestine of olive flounder and evaluate their differential expression profiles during Edwardsiella tarda infection, which is an important zoonotic and intestinal pathogen. A total of 4,445 putative lncRNAs were identified, including 3,975 novel lncRNAs and 470 annotated lncRNAs. These lncRNAs had shorter lengths and fewer exons compared with mRNAs. In total, 115 differentially expressed lncRNAs (DE-lncRNAs) were identified during E. tarda infection. To validate the expression pattern of lncRNAs, six DE-lncRNAs were randomly selected for quantitative real-time PCR. The co-located and co-expressed mRNAs of DE-lncRNAs were predicted, which were used to conduct the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. The target genes of DE-lncRNAs enriched numerous immune-related processes and exhibited a strong correlation with immune-related signaling pathways. To better understand the extensive regulatory functions of lncRNAs, the lncRNA–miRNA–mRNA regulatory networks were constructed, and two potential competing endogenous RNA (ceRNA) networks, LNC_001979-novel_171-Potusc2 and LNC_001979-novel_171-Podad1, were preliminarily identified from the intestine of olive flounders for the first time. In conclusion, this study provides an invaluable annotation and expression profile of lncRNAs in the intestine of olive flounder infected with E. tarda; this forms a basis for further studies on the regulatory function of lncRNAs in the intestinal mucosal immune responses of olive flounder.
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