Reich Shelley, Loschko Tobias, Jung Julie, Nestel Samantha, Sommer Ralf J, Werner Michael S
School of Biological Sciences, University of Utah, Salt Lake City, Utah 84112, USA.
Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany.
Genome Res. 2025 Jul 1;35(7):1560-1573. doi: 10.1101/gr.279783.124.
Developmental plasticity enables the production of alternative phenotypes in response to different environmental conditions. Although significant advances in understanding the ecological and evolutionary implications of plasticity have been made, understanding its genetic basis has lagged. However, a decade of genetic screens in the model nematode has culminated in the identification of more than 30 genes that affect mouth form. We also recently reported the critical window of environmental sensitivity and therefore have clear expectations for when differential gene expression should matter. Here, we collated existing data into a gene-regulatory network (GRN) and performed developmental transcriptomics across different environmental conditions, genetic backgrounds, and mutants to assess the regulatory logic of mouth-form plasticity. We find that only two genes in the GRN ( and ) are sensitive to the environment during the critical window. The time points of their sensitivity differ, suggesting that they act as sequential checkpoints. Additionally, / is differentially expressed across strains and species with different mouth-form biases, highlighting the potential role of switch-gene regulation in the evolution of plasticity. We also observe temporal constraint upon the transcriptional effects of mutating the GRN and reveal unexpected feedback between mouth-form genes. Finally, a comprehensive analysis of all samples identifies metabolism as a shared pathway for regulating mouth-form plasticity. These data are presented in a Shiny app to facilitate gene expression comparisons across development in up to 14 different conditions. Collectively, our results divide the GRN for mouth-form plasticity into environmentally sensitive switch genes and downstream genes that execute the decision.
发育可塑性能够使生物体根据不同的环境条件产生不同的表型。尽管在理解可塑性的生态和进化意义方面已经取得了重大进展，但对其遗传基础的理解却滞后了。然而，在模式线虫中进行的十年基因筛选最终鉴定出了30多个影响口器形态的基因。我们最近还报告了环境敏感性的关键窗口，因此对于差异基因表达何时起作用有了明确的预期。在这里，我们将现有数据整理成一个基因调控网络（GRN），并在不同的环境条件、遗传背景和突变体中进行发育转录组学研究，以评估口器形态可塑性的调控逻辑。我们发现，在关键窗口期间，GRN中只有两个基因（和）对环境敏感。它们的敏感时间点不同，这表明它们起着连续检查点的作用。此外，/在具有不同口器形态偏向的菌株和物种中差异表达，突出了开关基因调控在可塑性进化中的潜在作用。我们还观察到了GRN突变对转录效应的时间限制，并揭示了口器形态基因之间意想不到的反馈。最后，对所有样本的综合分析确定代谢是调节口器形态可塑性的共同途径。这些数据展示在一个Shiny应用程序中，以便于在多达14种不同条件下比较发育过程中的基因表达。总的来说，我们的结果将口器形态可塑性的GRN分为对环境敏感的开关基因和执行决策的下游基因。
