The Arabidopsis active demethylase ROS1 cis-regulates defence 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 find 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.

The epiallelic potential of transposable elements and its evolutionary significance in plants

“…Supporting this hypothesis, mutations in pathways involved in DNA methylation or demethylation of TEs affect resistance to pathogens [81,[116][117][118][119]. Moreover, upregulation of defence genes relies in many cases on active DNA demethylation of TE sequences located in their promoters [120,121]. Specifically, it was shown that ROS1 antagonizes the action of RdDM over transcription factor binding sites that are adjacent to TE sequences within the promoters of defence genes, thus exacerbating their induction in response to pathogen attacks [121].…”

“…Moreover, upregulation of defence genes relies in many cases on active DNA demethylation of TE sequences located in their promoters [120,121]. Specifically, it was shown that ROS1 antagonizes the action of RdDM over transcription factor binding sites that are adjacent to TE sequences within the promoters of defence genes, thus exacerbating their induction in response to pathogen attacks [121]. In addition, ROS1 expression itself is quantitatively and positively coupled to the DNA methylation level of a TE sequence located in the promoter of the gene, which as a result serves as an epigenetic rheostat or 'methylstat' [122,123].…”

Epigenetics: a catalyst of plant immunity against pathogens

“…The most straightforward mechanism is cis-regulation, whereby TE hypomethylation causes regional euchromatisation, which increases the accessibility of transcriptional machinery to nearby defence genes (Wilkinson et al, 2019). For example, DNA demethylation by ROS1 facilitates MAMP-induced expression of the disease resistance gene RMG1 by limiting RdDM at the 3' boundary of a TE-derived repeat sequence embedded in its promoter (Halter et al, 2021).…”

DNA methylation affects pre-mRNA transcriptional initiation and processing in Arabidopsis

“…It is known that DNA methylation in some promoter regions may prevent transcription initiation, since DNA methylation-sensitive transcription factors cannot bind to their targets on the promoters to start transcription (39). For example, for WRKY transcription factors to bind to defense gene promoters, they need Repressor of Silencing 1 (ROS1) to demethylate DNA (40). Since the DNA methylation related-mutants used in this study have genome-wide effects on DNA methylation, we wanted to see if we could uncover some cryptic promoters in the genomes of these mutants by ONT DRS.…”