Long Yong, Li Xixi, Li Fengyang, Ge Guodong, Liu Ran, Song Guili, Li Qing, Qiao Zhigang, Cui Zongbin
State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
University of Chinese Academy of Sciences, Beijing, China.
Front Genet. 2020 Sep 23;11:556418. doi: 10.3389/fgene.2020.556418. eCollection 2020.
Properly regulated transcriptional responses to environmental perturbations are critical for the fitness of fish. Although gene expression profiles in the tissues of common carp upon cold stress were previously characterized, the transcriptional programs underlying cold acclimation are still not well known. In this study, the ability of three common carp strains including Hebao red carp (HB), Songpu mirror carp (SPM) and Yellow river carp (YR) to establish cold resistance after acclimation to a mild hypothermia stress at 18°C for 24 h was confirmed by measurements of the critical thermal minimums (CTMin). The gene expression profiles of the brain and the heart from these strains under both control and cold-acclimated conditions were characterized with RNA-sequencing. The data of the three common carp strains with different genetic background were combined in the differential gene expression analyses to balance the effects of genetic diversity on gene expression. Marked effects of tissue origins on the cold-induced transcriptional responses were revealed by comparing the differentially expressed gene (DEG) lists of the two tissues. Functional categories including spliceosome and RNA splicing were highly enriched in the DEGs of both tissues. However, steroid biosynthesis was specifically enriched in DEGs of the brain and response to unfolded protein was solely enriched in DEGs of the heart. Consistent with the up-regulation of the genes involved in cholesterol biosynthesis, total cholesterol content of the brain was significantly increased upon cold stress. Moreover, cold-induced alternative splicing (AS) events were explored and AS of the (RNA-binding motif protein, X chromosome) gene was confirmed by real-time quantitative PCR. Finally, a core set of cold responsive genes (CRGs) were defined by comparative transcriptomic analyses. Our data provide insights into the transcriptional programs underlying cold acclimation of common carp and offer valuable clues for further investigating the genetic determinants for cold resistance of farmed fish.
对环境扰动进行适当调控的转录反应对于鱼类的适应性至关重要。尽管先前已对鲤鱼在冷应激下组织中的基因表达谱进行了表征，但冷驯化背后的转录程序仍不太清楚。在本研究中，通过测量临界低温最小值（CTMin），证实了包括荷包红鲤（HB）、松浦镜鲤（SPM）和黄河鲤（YR）在内的三种鲤鱼品系在18°C下适应轻度低温应激24小时后建立抗寒能力的情况。利用RNA测序对这些品系在对照和冷驯化条件下大脑和心脏的基因表达谱进行了表征。在差异基因表达分析中合并了具有不同遗传背景的三种鲤鱼品系的数据，以平衡遗传多样性对基因表达的影响。通过比较两个组织的差异表达基因（DEG）列表，揭示了组织来源对冷诱导转录反应的显著影响。包括剪接体和RNA剪接在内的功能类别在两个组织的DEG中高度富集。然而，类固醇生物合成在大脑的DEG中特异性富集，而对未折叠蛋白的反应仅在心脏的DEG中富集。与胆固醇生物合成相关基因的上调一致，冷应激后大脑中的总胆固醇含量显著增加。此外，还探索了冷诱导的可变剪接（AS）事件，并通过实时定量PCR证实了RNA结合基序蛋白X染色体（RBMX）基因的AS。最后，通过比较转录组分析定义了一组核心冷响应基因（CRG）。我们的数据为鲤鱼冷驯化背后的转录程序提供了见解，并为进一步研究养殖鱼类抗寒的遗传决定因素提供了有价值的线索。
