Wilkinson, S. W. | bioRxiv Science

bioRxiv2025

From recall to reset: the role of DNA (de)methylation in modulating plant immune memory

Immune memory enables plants to respond more effectively to recurrent pathogen infections. Epigenetic changes in DNA methylation and small RNAs have been implicated, yet how their temporal dynamics govern the establishment and erasure of immune memory remains unclear. Using a chemically inducible system in Arabidopsis to activate the DNA demethylase REPRESSOR OF SILENCING 1 (ROS1), we establish immune memory against biotrophic pathogens that persists for up to two weeks. Memory establishment coincides with reduced small RNA accumulation and DNA methylation along chromosome arms, revealing gene targets involved in salicylic acid-dependent immunity and DNA damage repair. These changes are progressively reversed during immune memory erasure. In contrast, transposon-rich pericentromeres retain elevated small RNA and DNA methylation levels, consistent with a CLASSY3-associated redistribution of RNA-directed DNA methylation. Our findings show that transient ROS1 activity drives contrasting epigenetic responses across chromosomal regions, shaping both the establishment and erasure of plant immune memory.

plant biology↗

bioRxiv2024

Multi-generational biotic stress increases the rate of spontaneous epimutations in a ROS1-dependent manner

Mistakes in the maintenance of CG methylation are a source of spontaneous epimutations in plants that can be inherited across generations. The extent to which these stochastic events are affected by prolonged exposure to biotic and abiotic stress remains poorly characterized. Here, we grew Arabidopsis Mutation Accumulation (MA) lines for 12 generations in the presence of two biotic stressors: Pseudomonas syringae (Pst) and salicylic acid (SA). We found that multi-generational exposure to Pst and SA led to an 18%-32% and 23%-61% increase in the genome-wide epimutation rate, respectively. These rate increases were mainly targeted to subsets of genes characterized by low steady-state methylation (LM), on average, and a lack of transcriptional responsiveness to stress. We show that these effects are mediated by the DNA demethylase Repressor of Silencing 1 (ROS1). Loss of ROS1 not only buffers transcriptional responses to biotic stress, but also stabilizes epimutation rates, particularly in LM genes, rendering them insensitive to environmental perturbations. Taken together, our data demonstrates that stress can induce heritable epimutations and highlights a ROS1-mediated link between transcriptional plasticity and DNA methylation maintenance fidelity over generations.

evolutionary biology↗