Differential Gene Expression Profiles and Alternative Isoform Regulations in Gill of Nile Tilapia in Response to Acute Hypoxia
Differential Gene Expression Profiles and Alternative Isoform Regulations in Gill of Nile Tilapia in Response to Acute Hypoxia
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尼罗罗非鱼鳃响应急性缺氧的差异基因表达谱和替代亚型调控
DOI：
10.1007/s10126-017-9774-4
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发表时间：
2017-12-01
影响因子：
3
通讯作者：
Xia, Jun Hong
中科院分区：
文献类型：
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作者：
Li, Hong Lian;Lin, Hao Ran;Xia, Jun Hong
鱼类经常遇到暴露于急性缺氧环境空间或时间。鳃器在鱼类对低氧胁迫的反应中起重要作用。关于鳃在低氧胁迫下的分子调控机制的研究较少。本研究通过RNA测序技术（RNA-Seq）研究了耐缺氧鱼类尼罗罗非鱼（Oreochromis niloticus）鳃对12 h急性缺氧的转录组学反应。我们对三个对照样本和三个缺氧处理样本的信使RNA进行了测序。生物信息学分析确定了239个差异表达基因（DEG）和34个基因（DUES），有显着的差异替代异构体调控事件在至少一个外显子区域在鳃响应急性缺氧。在缺氧处理下，在三个时间点（6，12，和24小时）采样的5个组织（心脏，肝脏，脑，鳃，脾）的时空表达分析证实了显着关联的差异外显子使用在两个DUES基因（TLDC 2和SSX 2 IPA）与缺氧条件。进一步的功能分析提示了几种能量和免疫反应相关的途径，例如，代谢途径和抗原加工与呈递，含有最丰富的DEG基因。我们发现在低氧胁迫下，DEG基因的一些GO生物学过程，如糖酵解、代谢过程、前体代谢物和能量的产生以及胆固醇代谢过程显著富集。我们的研究结果表明，丰富的差异基因表达的变化和替代异构体调控事件的基因参与在鳃缺氧反应。我们的研究结果为探讨鱼类低氧胁迫下基因调控机制提供了基础。
Fish often encounters exposures to acute environmental hypoxia either spatially or temporally. Gill organ plays important roles in response to hypoxic stress in fish. Few studies focus on the molecular regulation mechanisms of gills under hypoxic stress. In this study, we investigated the transcriptomic response to 12-h acute hypoxia in gill of a hypoxia tolerant fish, Nile tilapia Oreochromis niloticus through RNA sequencing (RNA-Seq). We sequenced messenger RNA from three control samples and three hypoxia-treated samples. Bioinformatics analysis identified 239 differentially expressed genes (DEG) and 34 genes (DUES) that had significant differential alternative isoform regulation events in at least one exonic region in gill in response to acute hypoxia. The spatiotemporal expression analysis in five tissues (heart, liver, brain, gill, and spleen) sampled at three time points (6, 12, and 24 h) under hypoxia treatment confirmed the significant association of differential exon usages in two DUES genes (TLDC2 and SSX2IPA) with hypoxia conditions. Further functional analysis suggested several energy and immune response-related pathways, e.g., metabolic pathway and antigen processing and presentation, contained the most abundant DEG genes. We found that some GO biological processes for DEG genes were significantly enriched under hypoxic stress, such as glycolysis, metabolic process, generation of precursor metabolites and energy, and cholesterol metabolic process. Our findings suggest abundant differential gene expression changes and alternative isoform regulation events in genes involved in the hypoxia response in gill. Our results provide a basis for exploring the gene regulation mechanism under hypoxic stress in fish.