The Arabidopsis demethylase ROS1 cis-regulates defense genes by erasing DNA methylation at promoter-regulatory regions

Abstract

Active DNA demethylation has emerged as an important regulatory process of plant and mammalian immunity. However, very little is known about the mechanisms by which active demethylation controls transcriptional immune reprogramming and disease resistance. Here, we first show that the Arabidopsis active demethylase ROS1 promotes basal resistance towards Pseudomonas syringae by antagonizing RNA-directed DNA methylation (RdDM). Furthermore, we found that ROS1 facilitates the flagellin-triggered induction of the disease resistance gene RMG1 by limiting RdDM at the 3 boundary of a remnant RC/Helitron transposable element (TE) embedded in its promoter. We further identify flagellin-responsive ROS1 putative primary targets, and show that at a subset of promoters, ROS1 erases methylation at discrete regions exhibiting WRKY transcription factors (TFs) binding. In particular, we demonstrate that ROS1 removes methylation at the orphan immune receptor RLP43 promoter, to ensure DNA binding of WRKY TFs. Finally, we show that ROS1-directed demethylation of the RMG1 and RLP43 promoters is causal for both flagellin responsiveness of these genes and for basal resistance. Overall, these findings significantly advance our understanding of how active demethylases shape transcriptional immune reprogramming to enable antibacterial resistance. HIGHLIGHTSO_LIThe TNL RMG1 that is regulated by ROS1 positively regulates basal resistance towards Pto DC3000 C_LIO_LIROS1 regulates the flg22-triggered differential expression of more than 2000 thousands genes, among which 10% are demethylated by ROS1 C_LIO_LIROS1 facilitates the transcriptional activation of a subset of flg22-induced genes by antagonizing RdDM at discrete promoter regions C_LIO_LIWRKY transcription factors (TFs) bind to the demethylated promoter regions of a subset of flg22-induced ROS1 targets C_LIO_LIThe hypermethylation at the RLP43 promoter, caused by the lack of ROS1, repels DNA binding of two PAMP-responsive WRKY TFs C_LIO_LISpecific hypermethylation at the ROS1-targeted promoter regions of RMG1 and RLP43 is causal for their silencing as well as for disease susceptibility against Pto DC3000 C_LI