Networks Regulating Hormone-Mediated Plant Growth

We are investigating hormone-mediated growth in Arabidopsis seedlings using genome-scale techniques, in order to understand the networks and signalling pathways regulating these processes. Our approaches include chromatin immunoprecipitation sequencing (ChIP-Seq) of 200 transcription factors (TFs) under native expression, in vitro determination TF DNA binding motifs, time series transcriptome analyses by RNA-Seq, genome-wide association studies, large-scale protein-protein interaction studies and forward genetics. Our initial studies have focused on responses to the phytohormone ethylene (ET), which has important roles in growth, development and defense. ET signalling involves a cascade of transcriptional reprogramming starting at EIN3, the master regulatory TF, which in turn activates RAV/EDF family TFs. EDF family TFs are involved in diverse plant defensive and hormonal pathways, and are potential novel integrators of hormone signalling and RNA silencing. We have revealed contrasting roles and functions of these TFs through sequential ChIP-Seq studies coupled to time-series RNA-Seq. Together they target the majority of the ET-responsive transcriptome. Data also indicates that EDF family members may have both unique and conserved functions. Currently, we are expanding our study to incorporate crosstalk with and between other hormone signalling pathways, by conducting ChIP-Seq on their primary TFs and by time series hormone response transcriptome profiling. Experiments have focused on the hormones jasmonic acid, salicylic acid and brassinosteroid. Results will be presented demonstrating how diverse data sources can be integrated to discover regulators of specific cohorts of hormone responsive genes. Furthermore, I will present data demonstrating the high degree of connectivity between diverse hormonal pathways.