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引用本文:朱婷芳,管峰,苗亮,史雨红,陈炯.大弹涂鱼(Boleophthalmus pectinirostris)单核巨噬细胞低氧胁迫比较转录组学分析.海洋与湖沼,2020,51(2):335-344.
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大弹涂鱼(Boleophthalmus pectinirostris)单核巨噬细胞低氧胁迫比较转录组学分析
朱婷芳1,2, 管峰2, 苗亮2,3, 史雨红2,3, 陈炯1,2,3
1.宁波大学 农产品质量安全危害因子与风险防控国家重点实验室 宁波 315832;2.宁波大学海洋学院 生物化学与分子生物学实验室 宁波 315832;3.宁波大学海洋学院 应用海洋生物技术教育部重点实验室 宁波 315832
摘要:
低氧是鱼类在水生环境中的关键压力之一。而大弹涂鱼(Boleophthalmus pectinirostris,mudskipper)可能是少数能在低氧中自然呼吸的脊椎动物。本研究中,我们分析了低氧胁迫8h后大弹涂鱼头肾源单核巨噬细胞(monocytes/macrophages,MO/MΦ)转录组变化。采用Illumina Hiseq 4000平台进行高通量测序,获得了大弹涂鱼MO/MΦ短时低氧胁迫相关的转录组数据,并将获得的原始数据上传至NCBI获得ID号:SRR9771486-SRR9771491(Bioproject PRJNA543702)。分析结果显示,P<0.05和|log2(fold change)|≥ 1条件下进行差异表达基因(differentially expressed genes,DEGs)筛选,低氧处理组中共获得4487个DEGs,包括2507个上调DEGs,1980个下调DEGs。其中低氧诱导因子(hypoxia-inducible factors,HIF)转录本的表达无显著变化,而血管内皮生长因子(vascular endothelial growth factor-A,VEGF-A)和3-磷酸甘油醛脱氢酶(glyceraldehyde 3-phosphate dehydrogenase,GAPDH)基因转录本表达上调。基因本体(Gene Ontology,GO)注释以及京都基因和基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)信号通路富集分析揭示了糖酵解/糖异生和氧化磷酸化可能在MO/MΦ应对短时低氧胁迫中具有重要作用。随机选择10个DEGs进行实时荧光定量PCR验证,上述基因表达变化趋势与转录组数据一致。本研究揭示了在短时低氧胁迫下大弹涂鱼MO/MΦ基因表达及信号通路调控机制。
关键词:  低氧胁迫  基因表达  信号通路  比较转录组学分析  大弹涂鱼
DOI:10.11693/hyhz20191100223
分类号:S917
基金项目:国家自然科学基金项目,31772876号,31402323号;宁波市科技创新团队项目,2015C110018号;宁波市自然科学基金项目,2018A610225号;宁波市科技富民项目,2017C10037号。
COMPARATIVE TRANSCRIPTOME ANALYSIS OF MO/MΦ IN RESPONSE TO LOW OXYGEN STRESS IN MUDSKIPPER BOLEOPHTHALMUS PECTINIROSTRIS
ZHU Ting-Fang1,2, GUAN Feng2, MIAO Liang2,3, SHI Yu-Hong2,3, CHEN Jiong1,2,3
1.State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315832, China;2.Laboratory of Biochemistry and Molecular Biology, School of Marine Science, Ningbo University, Ningbo 315832, China;3.Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Science, Ningbo University, Ningbo 315832, China
Abstract:
Hypoxia is one of the key pressures of fish in aquatic environment. And mudskipper (Boleophthalmus pectinirostris) might be one of a few vertebrates that naturally respire hypoxic air. Therefore, the expression changes of head kidney-derived monocytes/macrophages (MO/MΦ) transcripts in mudskipper were analyzed under hypoxia stress for 8h. Using Illumina Hiseq 4000 platform for high-throughput sequencing, the complete transcriptome data of mudskipper MO/MΦ were obtained, and uploaded to National Center for Biotechnology Information (NCBI) with the accession number of SRR9771486-SRR9771491 (Bioproject PRJNA543702). Results show that a total of 4487 differentially expressed genes (DEGs) with 2507 up-regulated DEGs, and 1980 down-regulated DEGs were obtained in hypoxia group, screening under the condition of P<0.05 and |log2(fold change)| ≥ 1. There was no significant change in the expression of hypoxia inducible factor (HIF) transcripts, but significant upregulation in the expression of vascular endothelial growth factor (VEGF-A) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) transcripts. The Gene Ontology (GO) annotation and Kyoto Encyclopedia of Gene and Genome (KEGG) signal pathway enrichment analysis revealed that glycolysis/gluconeogenesis and oxidative phosphorylation might play important roles in short-term hypoxia stress on MO/MΦ. Ten differentially expressed genes were randomly selected for quantitative real-time PCR (qRT-PCR) verification, and the trend was consistent with that of the transcriptome analysis. Finally, the regulation of gene expressions and the signal pathways in mudskipper MO/MΦ responding to short-term hypoxia stress have been revealed.
Key words:  hypoxia stress  gene expression  signal pathway  comparative transcriptome analysis  Boleophthalmus pectinirostris
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