Thorstensen Matt J, Turko Andy J, Heath Daniel D, Jeffries Ken M, Pitcher Trevor E
Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2.
Department of Biology, McMaster University, Hamilton, ON, Canada,L8S 4L8.
J Exp Biol. 2022 Jun 15;225(12). doi: 10.1242/jeb.244162. Epub 2022 Jun 27.
Transcriptomic research provides a mechanistic understanding of an organism's response to environmental challenges such as increasing temperatures, which can provide key insights into the threats posed by thermal challenges associated with urbanization and climate change. Differential gene expression and alternative splicing are two elements of the transcriptomic stress response that may work in tandem, but relatively few studies have investigated these interactions in fishes of conservation concern. We studied the imperilled redside dace (Clinostomus elongatus) as thermal stress is hypothesized to be an important cause of population declines. We tested the hypothesis that gene expression-splicing interactions contribute to the thermal stress response. Wild fish exposed to acute thermal stress were compared with both handling controls and fish sampled directly from a river. Liver tissue was sampled to study the transcriptomic stress response. With a gene set enrichment analysis, we found that thermally stressed fish showed a transcriptional response related to transcription regulation and responses to unfolded proteins, and alternatively spliced genes related to gene expression regulation and metabolism. One splicing factor, prpf38b, was upregulated in the thermally stressed group compared with the other treatments. This splicing factor may have a role in the Jun/AP-1 cellular stress response, a pathway with wide-ranging and context-dependent effects. Given large gene interaction networks and the context-dependent nature of transcriptional responses, our results highlight the importance of understanding interactions between gene expression and splicing for understanding transcriptomic responses to thermal stress. Our results also reveal transcriptional pathways that can inform conservation breeding, translocation and reintroduction programs for redside dace and other imperilled species by identifying appropriate source populations.
转录组学研究为理解生物体对环境挑战（如温度升高）的反应提供了一种机制，这可以为城市化和气候变化带来的热挑战所构成的威胁提供关键见解。差异基因表达和可变剪接是转录组应激反应的两个要素，它们可能协同作用，但相对较少的研究调查了受保护鱼类中的这些相互作用。我们研究了濒危的红边鲦鱼（Clinostomus elongatus），因为热应激被认为是种群数量下降的一个重要原因。我们测试了基因表达-剪接相互作用有助于热应激反应的假设。将暴露于急性热应激的野生鱼类与处理对照组和直接从河流中采样的鱼类进行比较。采集肝脏组织以研究转录组应激反应。通过基因集富集分析，我们发现热应激鱼类表现出与转录调控和对未折叠蛋白反应相关的转录反应，以及与基因表达调控和代谢相关的可变剪接基因。与其他处理组相比，一种剪接因子prpf38b在热应激组中上调。这种剪接因子可能在Jun/AP-1细胞应激反应中起作用，这是一个具有广泛且依赖于上下文的效应的途径。鉴于基因相互作用网络庞大以及转录反应具有依赖于上下文的性质，我们的结果强调了理解基因表达和剪接之间的相互作用对于理解转录组对热应激反应的重要性。我们的结果还揭示了转录途径，通过识别合适的源种群，可以为红边鲦鱼和其他濒危物种的保护育种、转移和重新引入计划提供信息。
