Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China.
Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, Guangdong, 524088, China.
Fish Shellfish Immunol. 2022 Nov;130:132-140. doi: 10.1016/j.fsi.2022.09.006. Epub 2022 Sep 7.
Non-coding RNAs (ncRNAs) have been implicated in a variety of biological processes. However, most ncRNAs are of unknown function and are as-yet unannotated. The immune-related functions of ncRNAs in the pearl oyster Pinctada fucata martensii were explored based on transcriptomic differences in the expression levels of long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) in the hemocytes of P.f. martensii after challenge by the pathogenic bacterium Vibrio parahaemolyticus. Across the challenged and control pearl oysters, 144 miRNAs and 14,571 lncRNAs were identified. In total, 13,375 ncRNAs were differentially expressed between the challenged and control pearl oysters; in the challenged pearl oysters as compared to the controls, 15 miRNAs and 5147 lncRNAs were upregulated, while 51 miRNAs and 8162 lncRNAs were downregulated. The sequencing results were validated using quantitative real-time polymerase chain reaction (qRT-PCR) analysis. GO and KEGG pathway analysis showed that genes targeted by the differentially expressed ncRNAs were associated with the vascular endothelial growth factor (VEGF) signaling pathway and the nuclear factor kappa-B (NF-κB) signaling pathway. An lncRNA-mRNA-miRNA network that was developed based on the transcriptomic results of this study suggested that lncRNAs may compete with miRNAs for mRNA binding sites. This study may provide a useful framework for the detection of additional novel ncRNAs, as well as new insights into the pathogenic mechanisms underlying the response of P.f. martensii to V. parahaemolyticus.
非编码 RNA（ncRNA）参与了多种生物学过程。然而，大多数 ncRNA 的功能未知，尚未被注释。本研究基于长链非编码 RNA（lncRNA）、微小 RNA（miRNA）和信使 RNA（mRNA）在感染副溶血弧菌后马氏珠母贝血细胞中转录组水平表达差异，探讨了 ncRNA 在马氏珠母贝免疫相关功能中的作用。在实验组和对照组马氏珠母贝中，共鉴定出 144 个 miRNA 和 14,571 个 lncRNA。实验组和对照组之间共鉴定出 13,375 个差异表达的 ncRNA；实验组中，15 个 miRNA 和 5,147 个 lncRNA 上调，51 个 miRNA 和 8,162 个 lncRNA 下调。采用实时荧光定量聚合酶链反应（qRT-PCR）分析对测序结果进行验证。GO 和 KEGG 通路分析表明，差异表达 ncRNA 靶向的基因与血管内皮生长因子（VEGF）信号通路和核因子 κB（NF-κB）信号通路有关。基于本研究转录组结果构建的 lncRNA-mRNA-miRNA 网络表明，lncRNA 可能与 miRNA 竞争 mRNA 结合位点。本研究为进一步检测新型 ncRNA 提供了有用的框架，为阐明马氏珠母贝对副溶血弧菌的反应机制提供了新的见解。
