College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair / Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China.
BMC Genomics. 2021 Sep 11;22(1):653. doi: 10.1186/s12864-021-07969-5.
As non-coding RNA molecules of more than 200 bp in length, long non-coding RNAs (lncRNAs) play a variety of roles in biological processes, including regulating the immune responses to bacterial infections. In recent years, there have been many in-depth studies on mammalian lncRNAs, but the relevant studies in fish are very limited. Meanwhile, since lncRNAs are not conserved among species, it is difficult to apply the existing results directly to unstudied species.
To obtain the information of lncRNAs in Megalobrama amblycephala, one of the most economically important freshwater fish in China, also to better understand the biological significance of lncRNAs in the immunity system, the fish liver at 0, 4, 12, 24, and 72 h post Aeromonas hydrophila infection (hpi) were obtained for lncRNA-sequencing (lncRNA-seq). A total of 14,849 lncRNAs were identified, and 2196 lncRNAs showed significant differences at different time points post A. hydrophila infection. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the target genes of the differentially expressed lncRNAs were enriched in several pathways related to immune such as apoptosis, inflammation, and immune response. Time-specific modules were then identified, using weighted correlation network analysis (WGCNA), and 28 modules significantly correlated with different time point after infection were found. Furthermore, four immune-related genes and six lncRNAs in the time-specific modules were subsequently verified by RT-qPCR.
The above findings reveal the discovery of widespread differentially expressed lncRNAs in the M. amblycephala liver post A. hydrophila infection, suggesting that lncRNAs might participate in the regulation of host response to bacterial infection, enriching the information of lncRNAs in teleost and providing a resources basis for further studies on the immune function of lncRNAs.
长非编码 RNA（lncRNA）是长度超过 200bp 的非编码 RNA 分子，在包括调节对细菌感染的免疫反应在内的各种生物过程中发挥多种作用。近年来，对哺乳动物 lncRNA 进行了大量深入研究，但鱼类相关研究非常有限。同时，由于 lncRNA 在物种间不保守，因此很难将现有结果直接应用于未研究的物种。
为了获得中国最重要的淡水经济鱼类之一——团头鲂（Megalobrama amblycephala）的 lncRNA 信息，也为了更好地了解 lncRNA 在免疫系统中的生物学意义，我们在嗜水气单胞菌（Aeromonas hydrophila）感染后 0、4、12、24 和 72 小时采集鱼肝脏进行 lncRNA 测序（lncRNA-seq）。共鉴定出 14849 个 lncRNA，其中 2196 个 lncRNA 在嗜水气单胞菌感染后不同时间点表现出显著差异。基因本体论（GO）注释和京都基因与基因组百科全书（KEGG）通路分析表明，差异表达 lncRNA 的靶基因富集在与免疫相关的几个通路中，如细胞凋亡、炎症和免疫反应。然后使用加权相关网络分析（WGCNA）对时间特异性模块进行鉴定，发现 28 个与感染后不同时间点显著相关的模块。此外，通过 RT-qPCR 进一步验证了时间特异性模块中的 4 个免疫相关基因和 6 个 lncRNA。
上述发现揭示了在团头鲂肝脏中广泛存在的差异表达 lncRNA 在嗜水气单胞菌感染后的发现，表明 lncRNA 可能参与宿主对细菌感染的反应调节，丰富了硬骨鱼类 lncRNA 的信息，并为进一步研究 lncRNA 的免疫功能提供了资源基础。
