Paneru Bam, Al-Tobasei Rafet, Palti Yniv, Wiens Gregory D, Salem Mohamed
Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, U.S.
Computational Science Program, Middle Tennessee State University, Murfreesboro, TN 37132, U.S.
Sci Rep. 2016 Oct 27;6:36032. doi: 10.1038/srep36032.
Bacterial cold-water disease caused by Flavobacterium psychrophilum is one of the major causes of mortality of salmonids. Three genetic lines of rainbow trout designated as ARS-Fp-R (resistant), ARS-Fp-C (control) and ARS-Fp-S (susceptible) have significant differences in survival rate following F. psychrophilum infection. Previous study identified transcriptome differences of immune-relevant protein-coding genes at basal and post infection levels among these genetic lines. Using RNA-Seq approach, we quantified differentially expressed (DE) long non-coding RNAs (lncRNAs) in response to F. psychrophilum challenge in these genetic lines. Pairwise comparison between genetic lines and different infection statuses identified 556 DE lncRNAs. A positive correlation existed between the number of the differentially regulated lncRNAs and that of the protein-coding genes. Several lncRNAs showed strong positive and negative expression correlation with their overlapped, neighboring and distant immune related protein-coding genes including complement components, cytokines, chemokines and several signaling molecules involved in immunity. The correlated expressions and genome-wide co-localization suggested that some lncRNAs may be involved in regulating immune-relevant protein-coding genes. This study provides the first evidence of lncRNA-mediated regulation of the anti-bacterial immune response in a commercially important aquaculture species and will likely help developing new genetic markers for rainbow trout disease resistance.
由嗜冷黄杆菌引起的细菌性冷水病是鲑科鱼类死亡的主要原因之一。三种虹鳟鱼遗传品系，即ARS-Fp-R（抗性）、ARS-Fp-C（对照）和ARS-Fp-S（易感），在感染嗜冷黄杆菌后的存活率上有显著差异。先前的研究确定了这些遗传品系在基础水平和感染后水平上免疫相关蛋白质编码基因的转录组差异。利用RNA测序方法，我们对这些遗传品系中响应嗜冷黄杆菌攻击的差异表达长链非编码RNA（lncRNA）进行了定量分析。遗传品系与不同感染状态之间的成对比较确定了556个差异表达的lncRNA。差异调节的lncRNA数量与蛋白质编码基因数量之间存在正相关。一些lncRNA与其重叠、相邻和远距离的免疫相关蛋白质编码基因（包括补体成分、细胞因子、趋化因子和一些参与免疫的信号分子）表现出强烈的正负表达相关性。相关表达和全基因组共定位表明，一些lncRNA可能参与调节免疫相关蛋白质编码基因。本研究首次证明了lncRNA介导对一种重要商业养殖水产动物抗菌免疫反应的调控，可能有助于开发虹鳟鱼抗病性的新遗传标记。
