Table_1_Acute hypoxia changes the gene expression profiles and alternative splicing landscape in gills of spotted sea bass (Lateolabrax maculatus).xlsx

Hypoxia is one of the most important environmental stressors in aquatic ecosystems. To deal with the hypoxia environment, fishes exhibit a series of physiological and molecular responses to maintain homeostasis and organism functions. In the present study, hypoxia-induced changes in gene expression profiles and alternative splicing (AS) events in spotted sea bass (Lateolabrax maculatus), a promising marine-culture fish species in China, were thoroughly investigated by RNA-Seq analysis. A total of 1,242, 1,487 and 1,762 differentially expressed genes (DEGs) were identified at 3 h, 6 h and 12 h in gills after hypoxia stress. Functional enrichment analysis by KEGG and GSEA demonstrated that HIF signal network system was significantly activated and cell cycle process was remarkably suppressed in response to hypoxia. According to the temporal gene expression profiles, six clusters were generated and protein-protein interaction (PPI) networks were constructed for the two clusters that enriched with hypoxia-induced (cluster 2) or -suppressed genes (cluster 5), respectively. Results showed that HIF signaling related genes including vegfa, igf1, edn1, cox2b, cxcr4b, ctnnb1, and slc2a1a, were recognized as hubs in cluster 2, while mcm2, chek1, pole, mcm5, pola1, and rfc4, that tightly related to cell cycle, were down-regulated and considered as hubs in cluster 5. Furthermore, a total of 410 differential alternative splicing (DAS) genes were identified after hypoxia, which were closely associated with spliceosome. Of them, 63 DAS genes also showed differentially expressed levels after hypoxia, suggesting that their expression changes might be regulated by AS mechanism. This study revealed the key biological pathways and AS events affected by hypoxia, which would help us to better understand the molecular mechanisms of hypoxia response in spotted sea bass and other fish species.

低氧是水生生态系统中最为关键的环境胁迫因子之一。为适应低氧环境，鱼类会启动一系列生理与分子应答反应，以维持机体稳态与正常生理功能。本研究以我国极具海水养殖潜力的经济鱼类——花鲈（Lateolabrax maculatus）为研究对象，通过RNA测序（RNA-Seq）技术系统解析了低氧胁迫下其基因表达谱与可变剪接（alternative splicing, AS）事件的变化规律。低氧胁迫处理后3、6、12小时，其鳃组织中分别鉴定出1242、1487和1762个差异表达基因（differentially expressed genes, DEGs）。通过京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）与基因集富集分析（Gene Set Enrichment Analysis, GSEA）开展功能富集分析，结果显示：低氧胁迫下低氧诱导因子（Hypoxia-inducible factor, HIF）信号网络系统被显著激活，而细胞周期进程则受到明显抑制。基于时序基因表达谱，研究人员将差异表达基因划分为6个表达聚类，并分别针对富集低氧诱导基因的聚类2与富集低氧抑制基因的聚类5构建了蛋白质-蛋白质相互作用（protein-protein interaction, PPI）网络。分析结果表明，聚类2中的核心枢纽基因以HIF信号通路相关基因为主，包括vegfa、igf1、edn1、cox2b、cxcr4b、ctnnb1及slc2a1a；而聚类5中与细胞周期密切相关的mcm2、chek1、pole、mcm5、pola1及rfc4等基因则呈现显著下调，并作为该聚类的核心枢纽基因存在。此外，本研究共鉴定出410个低氧胁迫下的差异可变剪接（differential alternative splicing, DAS）基因，这些基因显著富集于剪接体通路。其中，63个DAS基因同时呈现差异表达特征，提示其表达水平的变化可能由可变剪接机制调控。本研究揭示了低氧胁迫影响的关键生物学通路与可变剪接事件，可为进一步阐明花鲈及其他鱼类应对低氧胁迫的分子调控机制提供重要参考。