Transcript profiling upon overexpressing an AP2/ERF transcription factor Rap2.9 in A. thaliana

The genome of Arabidopsis contains 122 ERF transcription factor genes, some of which play diverse roles in the development and stress responses. A previous transcriptome analysis of Arabidopsis revealed that gene expression under combinatory stress conditions is not predictable from the combination of individual stresses (GSE46760). Searching for commonly regulated genes verified that only 11 genes were regulated in all stress combinations . Among these 11 genes, Rap2.9 (AT4G06746) was down-regulated under all stress conditions. Transgenic Arabidopsis thaliana lines overexpressing Rap2.9 under CaMV 35S promotor were generated, and the microarray analysis revealed that overexpression of Rap2.9 in A. thaliana plants causes massive reprogramming of transcription resulting in the alteration of the hormonal homeostasis and imbalances in signalling cascades related to stress response. Further analysis also revealed that Rap2.9 played an crucial role in plant development and stress tolerance in Arabidopsis plants. For microarray analysis, transgenic Arabidopsis plants (35S::Rap2.9-GFP) and wild-type plants (Col-0) were grown in the same time and same condition for 54 days. Leaf samples were immediately frozen in liquid nitrogen and stored at -80°C. For each genotype, 4 biological replicates have been sampled for RNA extraction.