Transcriptome profiling of mkk3-1 and mpk7_ko3 seeds in Arabidopsis thaliana

Seeds establish dormancy to delay germination until the arrival of a favorable growing season. In this study, we identify a fate switch comprised of the MKK3–MPK7 kinase cascade and the ethylene response factor ERF4 that is responsible for the seed state transition from dormancy to germination. We show that dormancy-breaking factors activate the MKK3–MPK7 module, which affects the expression of some a-EXPANSIN (EXPA) genes to control seed dormancy. Furthermore, we identify a direct downstream substrate of this module, ERF4, which suppresses the expression of these EXPAs by directly binding to the GCC boxes in their exon regions. The activated MKK3–MPK7 module phosphorylates ERF4, leading to its rapid degradation and thereby releasing its inhibitory effect on the expression of these EXPAs. Collectively, our work identifies a signaling chain consisting of protein phosphorylation, degradation, and gene transcription, by which the germination promoters within the embryo sense and are activated by germination signals from ambient conditions. Overall design: Comparative gene expression profiling analysis of RNA-seq data for dry and imbibed seeds of wildtype Col-0 and mutant mkk3-1 and mpk7_ko3.