Study of expression changes and alternative splicing events during RPS4-mediated resistance in Arabidopsis using a temperature-inducible system which mirrors pathogen-infection. Arabidopsis thaliana

Innate immune responses of plant cells confer the first line of defence against pathogens. Signals generated by activated receptors are integrated inside the cell and converge on transcriptional programmes in the nucleus. The Arabidopsis Toll-related intracellular receptor RPS4 operates inside nuclei to trigger resistance and defence gene reprogramming through the stress response regulator, EDS1. Using a combinaison of ChIP-seq and gene expression microarray profiling, we found that RPS4 associates with the genomic coding sequence of (mainly) defense-associated genes whose expression is subsequently strongly upregulated. Using RNA-seq, we tested wether the association pattern of RPS4 to its targets correlates with alternative splicing of similar sets of genes. Overall design: We used transgenic Arabidopsis plants over-expressing RPS4, a genetic background in which an immune response can be turned on rapidly and synchronously in leaf cells after a switch from high to moderate temperature. In order to substract defense-unrelated artifacts due to the temperature stimulus, we used Col-0 WT plants in parallel as negative control. This Series represents the RNA-Seq data only. The related gene expression microarray data are available in GSE40143, and ChIP-Seq data in GSE40329.