Valenzuela-Miranda Diego, Valenzuela-Muñoz Valentina, Farlora Rodolfo, Gallardo-Escárate Cristian
Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P. O. Box 160-C, Concepción, Chile.
Laboratorio de Biotecnología Acuática y Genómica Reproductiva/Instituto de Biología, Facultad de Ciencias Universidad de Valparaíso, Chile.
Dev Comp Immunol. 2017 Dec;77:287-296. doi: 10.1016/j.dci.2017.08.016. Epub 2017 Sep 1.
MicroRNAs (miRNAs) are small non-coding RNAs that have emerged as key regulators in diverse biological processes across taxa. However, despite the importance of these transcripts, little is known about their role during the immune response in salmonids. Because of this, we use deep sequencing technologies to explore the microRNA-based transcriptomic response of the Atlantic salmon (Salmo salar) to the intracellular bacteria Piscirickettsia salmonis, one of the main threats to salmon aquaculture in Chile. Hence, 594 different miRNAs were identified from head kidney and spleen transcriptomic data. Among them, miRNA families mir-181, mir-143 and mir-21 were the most abundant in control groups, while after infection with P. salmonis, mir-21, mir-181 and mir-30 were the most predominant families. Furthermore, transcriptional analysis revealed 84 and 25 differentially expressed miRNAs in head kidney and spleen respectively, with an overlapping response of 10 miRNAs between the analyzed tissues. Target prediction, coupled with GO enrichment analysis, revealed that the possible targets of the most regulated miRNAs were genes involved in the immune response, such as cortisol metabolism, chemokine-mediated signaling pathway and neutrophil chemotaxis genes. Among these, predicted putative target genes such as C-C motif chemokine 19-like, stromal cell-derived factor 1-like, myxovirus resistance protein 2 and hepcidin-1 were identified. Overall, our results suggest that miRNA expression in co-modulation with transcription activity of target genes is related to putative roles of non-coding RNAs in the immune response of Atlantic salmon against intracellular bacterial pathogens.
微小RNA（miRNA）是一类小型非编码RNA，已成为不同生物类群中多种生物学过程的关键调节因子。然而，尽管这些转录本很重要，但关于它们在鲑科鱼类免疫反应中的作用却知之甚少。因此，我们利用深度测序技术来探究大西洋鲑（Salmo salar）对细胞内细菌鲑鱼立克次氏体（Piscirickettsia salmonis）的基于微小RNA的转录组反应，该细菌是智利鲑鱼养殖的主要威胁之一。由此，从头部肾脏和脾脏转录组数据中鉴定出了594种不同的miRNA。其中，miR-181、miR-143和miR-21家族在对照组中最为丰富，而在感染鲑鱼立克次氏体后，miR-21、miR-181和miR-30家族最为突出。此外，转录分析分别揭示了头部肾脏和脾脏中有84种和25种差异表达的miRNA，在所分析的组织之间有10种miRNA存在重叠反应。靶标预测与GO富集分析相结合，揭示了受调控程度最高的miRNA的可能靶标是参与免疫反应的基因，如皮质醇代谢、趋化因子介导的信号通路和中性粒细胞趋化基因。其中，鉴定出了预测的假定靶标基因，如C-C基序趋化因子19样、基质细胞衍生因子1样、抗黏液病毒蛋白2和铁调素-1。总体而言，我们的结果表明，miRNA表达与靶基因转录活性的共同调节与非编码RNA在大西洋鲑针对细胞内细菌病原体的免疫反应中的假定作用有关。
