Understanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigated the signalling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA, which spans from the activity of master and secondary regulatory transcription factors, through gene expression outputs and alternative splicing, to protein abundance changes, protein phosphorylation and chromatin remodelling. We integrated time-series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enabled us to predict previously unknown points of crosstalk of JA to other signalling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behaviour, the general principles of which provide a framework for analyses of cross-regulation between other hormone and stress signalling pathways.

了解激素转录反应的系统级作用可以深入了解基因组如何重新编程以响应环境刺激。在这里，我们研究了激素茉莉酸 (JA) 的信号通路，它控制着植物中过多的至关重要的过程，并由转录因子 MYC2 及其在拟南芥中的近亲精心策划. 我们生成了一个对 JA 反应的综合框架，该框架从主调控转录因子和二级调控转录因子的活性，通过基因表达输出和可变剪接，到蛋白质丰度变化、蛋白质磷酸化和染色质重塑。我们将时间序列转录组分析与（磷酸）蛋白质组数据相结合，以重建基因调控网络模型。这些使我们能够预测 JA 与其他信号通路之间以前未知的串扰点，并确定 JA 调控机制的新组成部分，我们通过靶向突变分析对其进行了验证。这些结果提供了对植物激素如何重塑细胞功能和植物行为的全面理解，