Cold priming reshapes DNA methylation and transcriptional memory in Arabidopsis thaliana

Abstract Stress priming is a critical adaptive mechanism that enables plants to enhance responses to recurring environmental stresses. Although transcriptomic changes associated with cold stress priming have been reported, the underlying epigenetic mechanisms remain largely unknown. Here, we investigated transcriptomic and DNA methylation dynamics in cold priming in Arabidopsis thaliana . Cold stress induced distinct transcriptional responses in primed and non-primed plants and was accompanied by widespread DNA methylation changes, particularly in non-CG contexts, across both protein-coding genes and transposable elements (TEs). Genes exhibiting transcriptional memory were associated with lower gene-body DNA methylation than non-primed genes. Furthermore, DNA methylation mutants exhibited altered cold stress memory, supporting a role for DNA methylation in preventing inappropriate gene activation and maintaining the specificity of priming responses. Notably, the CG methylation-deficient mutant met1 exhibited enhanced activation of cold-responsive genes, including genes in the CBF pathway. Together, our findings suggest that DNA methylation contributes to cold stress memory by maintaining transcriptional precision in Arabidopsis .