The priming fingerprint on the plant transcriptome investigated through meta-analysis of RNA-Seq data

Plants may enter into a state of alert that allows them to deploy defensive measures in a more effective way upon stress occurrence. This phenomenon is termed defense priming, and it is started in plants with a still enigmatic priming phase in which complex molecular and physiological changes occur. During the priming phase the plant transcriptome is deeply affected, but it remains largely unclear the extent of the transcriptional changes that contribute to prime the plant. In this study, we performed a meta-analysis of publicly available RNA-Seq data obtained during different priming conditions and in different plant species in order to investigate the existence of a transcriptional “priming fingerprint”. Our results show that similarities in transcriptome reprogramming affect a small group of genes with similar and often low fold change value. Similarities affect, among others, the down-regulation of genes involved in methylerythritol 4-phosphate (MEP) pathway (e.g. DXR), photosynthesis (e.g. PSBQ-2), fatty acid synthesis (e.g. FAD2), and transcription factors (TFs) enabling normal development (e.g. BES1, DAR2, COL9), likely reflecting eventual metabolic costs. In contrast, the up-regulation of genes encoding receptors (e.g. RPM1), MAP kinases (MKK2, MPK6, MPK1), TFs enabling defense (e.g. RAP2.12, EIN3, WRKY18, HSFA4A, HSF3, BZIP17), genes involved in beta-oxidation (ACX1), monoterpene synthesis (GPS1), and negative immune signaling regulators (e.g. PP2C38 and BIR1) highlight a common preparation for a broad-spectrum defense. This study reveals a set of conserved transcriptional changes that mark the priming phase in plants, and aids to decipher the role of the transcriptome within the priming changes.