Transcription factor activity in cross-regulation between seedling hormone responses

Cross-regulation between hormone signalling pathways is indispensable for plant growth and development. However, the molecular mechanisms by which multiple hormones interact and co-ordinate activity are poorly understood. Here, we generated a cross-regulation network explaining how hormone signals are integrated from multiple pathways in etiolated Arabidopsis (Arabidopsis thaliana) seedlings. To do so we comprehensively characterized transcription factor activity during plant hormone responses and reconstructed dynamic transcriptional regulatory models for six hormones; abscisic acid, brassinosteroid, ethylene, jasmonic acid, salicylic acid and strigolactone/karrikin. These models incorporated target data for hundreds of transcription factors coupled with thousands of protein-protein interactions. Each hormone recruited different combinations of transcription factors, a subset of which were shared between hormones. Hub target genes existed within hormone transcriptional networks, exhibiting transcription factor activity themselves. A group of MITOGEN-ACTIVATED PROTEIN KINASES were also identified as potential key points of cross-regulation between multiple hormones. Loss of functional MPK6 disrupted the global proteome and phosphoproteome, and transcriptome in the response to hormones. Finally, we determined that all hormones drive substantial alternative splicing that has distinct effects on the transcriptome compared with differential gene expression, acting in early hormone responses. These results provide a comprehensive understanding of the common features of plant transcriptional regulatory pathways and how cross-regulation between hormones acts upon gene expression. Overall design: ChIP-seq and RNA-seq were applied to comprehensively profile the transcriptional regulation in response to multiple hormones in Col-0 and mpk6 mutants seedlings