Identification and characterization of immune-related microRNAs in blunt snout bream, Megalobrama amblycephala
Identification and characterization of immune-related microRNAs in blunt snout bream, Megalobrama amblycephala
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团头鲂免疫相关 microRNA 的鉴定和表征
DOI：
10.1016/j.fsi.2015.12.013
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发表时间：
2016-02-01
影响因子：
4.7
通讯作者：
Yan Jinpeng
中科院分区：
文献类型：
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作者：
Jiang Yuhong;Tang Leilei;Yan Jinpeng
microRNA（miRNAs）在多种生物过程中发挥着重要作用，包括免疫反应。团头鲂（Megalobrama amblycephala）是我国集约化混养系统中的一种重要经济鱼类。目的鉴定M.在团头鲂（Amblycephala）中，构建了脂多糖（LPS）刺激和非脂多糖刺激免疫组织的两个小RNA（sRNA）文库，并利用高通量测序技术进行了测序。在正常文库和感染文库中分别获得了16，425，543和15，076，813个原始读段，对应于14，156，755和13，445，869个干净读段。通过生物信息学分析，共鉴定出324种miRNAs，其中已知miRNAs 218种，新发现miRNAs 106种。我们使用成对比较分析了两个文库之间差异表达的miRNA。结果表明，113个（34.88%）miRNAs在两个文库中有显著差异表达，其中63个（55.75%）在LPS刺激样品中表达升高。其中，一些已知的miRNAs被鉴定为与免疫相关。对两个样本的12个miRNAs进行实时定量PCR（RT-qPCR），测序结果与RT-qPCR结果一致。利用计算预测法预测可能受这些差异表达的miRNAs调控的靶基因。通过基因本体富集（GO）和京都基因百科全书和基因组通路分析（KEGG）对靶基因进行功能注释，发现大部分差异miRNAs可能参与免疫应答。据我们所知，这是第一个全面的研究miRNA在响应LPS刺激M。团头菌，甚至是鱼类这些结果加深了我们对miRNAs在复杂的宿主免疫系统中的作用的理解，并将有助于开发新的控制策略，用于宿主对各种细菌入侵的免疫防御。团头虫(C)2016爱思唯尔有限公司版权所有
MicroRNAs (miRNAs) play vital roles in diverse biological processes, including in immune response. Blunt snout bream (Megalobrama amblycephala) is a prevalent and important commercial endemic freshwater fish species in China's intensive polyculture systems. To identify immune-related miRNAs of M. amblycephala, two small RNA (sRNA) libraries from immune tissues with or without lipopolysaccharide (LPS) stimulation were constructed and sequenced using the high-throughput sequencing technology. Totally, 16,425,543 and 15,076,813 raw reads, corresponding to 14,156,755 and 13,445,869 clean reads, were obtained in the normal and infected libraries, respectively. A total of 324 miRNAs, including 218 known miRNAs and 106 putative novel miRNAs were identified by bioinformatic analysis. We analyzed differentially expressed miRNAs between two libraries using pairwise comparison. 113 (34.88%) miRNAs were found to be significantly differentially expressed between two libraries, with 63 (55.75%) exhibiting elevated expression in LPS stimulation sample. Thereinto, a number of known miRNAs were identified immune-related. Real-time quantitative PCR (RT-qPCR) were implemented for 12 miRNAs of two samples, and agreement was confirmed between the sequencing and RT-qPCR data. Target genes likely regulated by these differentially expressed miRNAs were predicted using computational prediction. The functional annotation of target genes by Gene Ontology enrichment (GO) and Kyoto Encyclopedia of Genes and Genomes pathway analysis (KEGG) indicated that a majority of differential miRNAs might involved in immune response. To our knowledge, this is the first comprehensive study of miRNAs in response to LPS stimulation in M. amblycephala, even in fish. These results deepened our understanding of the role of miRNAs in the intricate host's immune system, and should be useful to develop new control strategies for host immune defense against various bacterial invasions in M. amblycephala. (C) 2016 Elsevier Ltd. All rights reserved.