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The ethylene transcriptional response mediated by ETHYLENE INSENSITIVE3 in Arabidopsis thaliana


The sessile nature of plants necessitates a phenotypic plasticity that enables plants to respond to changes in environment throughout growth and development. Orchestration of molecular components at various levels in a spatial and temporal dimension is required. However, how signals are integrated to produce a specific response, e.g. how a simple hydrocarbon, the plant hormone ethylene, can cause a diverse set of morphological response, remains elusive. To better understand the integration of signals involved in generating these phenotypes, we characterized the transcriptional regulation of the ethylene response by identifying key protein-DNA interactions and transcriptional profiles in a temporal manner. The plant hormone ethylene regulates numerous growth and developmental processes in plants, including stem cell division, differential cell growth, stress response, response to pathogens, germination, senescence, fruit ripening and the triple response. The triple response, a decrease in cellular elongation, increase in radial swelling, and an exaggerated apical hook, has been the hallmark of the ethylene response in dark grown seedlings. To determine the molecular mechanisms of the ethylene response, we characterized the dynamic ethylene transcriptional response in etiolated seedlings. We identified targets of the master regulator of the ethylene signaling pathway, ETHYLENE INSENSITIVE3 (EIN3), using temporal chromatin immunoprecipitation sequencing (ChIP- Seq) and transcript sequencing (mRNA-Seq). First we identified the minimum complement of genes required for the ethylene transcriptional response in etiolated seedlings. Then we characterized targets of EIN3 based on their transcriptional state as well as their function in relation of the ethylene signaling pathway and response. We found a singular EIN3 binding pattern that increased upon ethylene treatment, which did not correspond to target gene transcription. Binding of EIN3 established feedforward transcriptional cascades, feedback circuitry of the ethylene signaling pathway, and interconnections between hormone response pathways at a multitude of levels, e.g. hormone biosynthesis, signal reception, signaling, and transcriptional response. Finally, we showed that mutants in a gene family targeted by EIN3 exhibit hormone response phenotypes in several developmental stages, thus demonstrating the integral role EIN3 plays in the orchestration of hormone crosstalk in plant growth and development

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