27Understanding the systems-level actions of transcriptional responses to hormones provides 28 insight into how the genome is reprogrammed in response to environmental stimuli. Here, we 29 investigate the signaling pathway of the hormone jasmonic acid (JA), which controls a plethora of 30 critically important processes in plants and is orchestrated by the transcription factor MYC2 and 31 its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the 32 response to JA that spans from the activity of master and secondary-regulatory transcription 33 factors, through gene expression outputs and alternative splicing to protein abundance changes, 34 protein phosphorylation and chromatin remodeling. We integrated time series transcriptome 35 analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These 36 enable us to predict previously unknown points of crosstalk from JA to other signaling pathways 37 and to identify new components of the JA regulatory mechanism, which we validated through 38 targeted mutant analysis. These results provide a comprehensive understanding of how a plant 39 hormone remodels cellular functions and plant behavior, the general principles of which provide 40 a framework for analysis of cross-regulation between other hormone and stress signaling 41 pathways. 42 43 44 45 46 47 48 49 50 51 52 5 2004, Fernandez-Calvo et al. , 2011). myc3 and myc4 single mutants behave like wildtype with 104 regards to JA-induced root growth inhibition. However, in combination with the myc2 mutant, 105 myc2 myc3 double mutants exhibit an increased JA hyposensitivity, almost as pronounced as in 106 myc2 myc3 myc4 triple mutants (Fernandez-Calvo et al., 2011). We consequently selected MYC3 107 for an in-depth analysis.
108In order to better understand how the master TFs MYC2 and MYC3 control the JA-109 induced transcriptional cascade, we determined their genome-wide binding sites using chromatin 110 immunoprecipitation sequencing (ChIP-seq). Four biological replicates of JA-treated (2 hours) 111 three-day-old etiolated Arabidopsis seedlings that express a native promoter-driven and epitope 112 (YPet)-tagged version of MYC2 and three biological replicates of MYC3 (Col-0 MYC2::MYC2-113 Ypet, Col-0 MYC3::MYC3-Ypet) were used (Gimenez-Ibanez et al., 2017). The genome-wide 114distributions of MYC2 and MYC3 binding sites were highly similar (Fig. 1c, d). We identified 6,736 115 MYC2 and 3,982 MYC3 binding sites of high confidence, equating to 6,178 MYC2 and 4,092