Contrasting epigenetic dynamics in chromosome arms and pericentromeres during ROS1-induced plant immune memory

Abstract 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 immune memory establishment and erasure remains unclear. Using a chemically inducible system to activate the DNA demethylase REPRESSOR OF SILENCING 1 (ROS1) in Arabidopsis, we establish immune memory against biotrophic pathogens that persists for at least one week. Memory establishment coincides with reduced small RNA accumulation and DNA methylation along chromosome arms, including at promoters of genes 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.