Boltaña Sebastian, Valenzuela-Miranda Diego, Aguilar Andrea, Mackenzie Simon, Gallardo-Escárate Cristian
Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile.
Institute of Aquaculture, University of Stirling, Stirling, UK.
Sci Rep. 2016 Mar 4;6:22698. doi: 10.1038/srep22698.
Despite evidence for participation in the host response to infection, the roles of many long non-coding RNAs (lncRNAs) remain unknown. Therefore, the aims of this study were to identify lncRNAs in Atlantic salmon (Salmo salar) and evaluate their transcriptomic regulation during ISA virus (ISAV) infection, an Orthomyxoviridae virus associated with high mortalities in salmonid aquaculture. Using next-generation sequencing, whole-transcriptome analysis of the Salmo salar response to ISAV infection was performed, identifying 5,636 putative lncRNAs with a mean length of 695 base pairs. The transcriptional modulation evidenced a similar number of differentially expressed lncRNAs in the gills (3,294), head-kidney (3,275), and liver (3,325) over the course of the infection. Moreover, analysis of a subset of these lncRNAs showed the following: (i) Most were similarly regulated in response to ISA virus infection; (ii) The transcript subsets were uniquely modulated in each tissue (gills, liver, and head-kidney); and (iii) A subset of lncRNAs were upregulated for each tissue and time analysed, indicating potential markers for ISAV infection. These findings represent the first discovery of widespread differential expression of lncRNAs in response to virus infection in non-model species, suggesting that lncRNAs could be involved in regulating the host response during ISAV infection.
尽管有证据表明许多长链非编码RNA（lncRNA）参与了宿主对感染的反应，但其作用仍不明确。因此，本研究的目的是鉴定大西洋鲑（Salmo salar）中的lncRNA，并评估其在感染传染性鲑鱼贫血病毒（ISAV）期间的转录组调控，ISAV是一种与鲑鱼养殖中高死亡率相关的正粘病毒科病毒。利用下一代测序技术，对大西洋鲑对ISAV感染的全转录组进行了分析，鉴定出5636个推定的lncRNA，平均长度为695个碱基对。转录调控表明，在感染过程中，鳃（3294个）、头肾（3275个）和肝脏（3325个）中差异表达的lncRNA数量相似。此外，对这些lncRNA的一个子集进行分析后发现：（i）大多数lncRNA对ISAV感染的反应调控方式相似；（ii）转录本子集在每个组织（鳃、肝脏和头肾）中受到独特调控；（iii）在分析的每个组织和时间点，都有一个lncRNA子集上调，这表明它们可能是ISAV感染的潜在标志物。这些发现首次揭示了非模式物种中lncRNA在病毒感染时广泛存在差异表达，表明lncRNA可能参与了ISAV感染期间宿主反应的调控。
