The jasmonate-response genome regulatory program is defined by the direct targets of transcription factors MYC2 and MYC3, chromatin modification and gene expression changes
Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing
Summary
The hormone jasmonic acid (JA) controls a plethora of crucially important processes in plants through a signaling pathway orchestrated by the transcription factor MYC2 and its closest relatives. Understanding the systems-level actions of transcription factors provides insight into how the genome is reprogrammed in response to environmental stimuli. However, deeper biological insight can be obtained if transcription factor activity is set in the broader regulatory context of the cell and the downstream organismal phenotypes the transcription factors control. Here, we have investigated the MYC2-governed genome regulatory network that controls JA responses in Arabidopsis thaliana etiolated seedlings. We have generated an integrated framework of the response to JA that 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 remodeling. We have integrated time series transcriptome analysis with (phospho)proteomic data using gene regulatory network models. These enable us to predict previously unknown points of crosstalk from JA to other signaling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant studies. The result is a comprehensive understanding of how a plant hormone remodels cellular function and plant behavior, the general principles of which provide a framework for analysis of cross-regulation between other hormone and stress signaling pathways.
Overall design
ChIP-seq, DAP-seq and RNA-seq was applied to comprehensively profile the chromatin landscape in Col-0 and myc2 mutants.
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