Transcriptome and epigenome dynamics underpin cold stress priming in Arabidopsis

Abstract

Stress priming is a critical adaptive mechanism that enables plants to enhance responses to recurring environmental stresses. While 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 during cold priming in Arabidopsis thaliana. Cold stress induces distinct gene expression patterns between primed and non-primed plants, accompanied by DNA methylation changes across all cytosine contexts in both protein-coding genes and transposable elements (TEs). Furthermore, DNA methylation mutants exhibit altered cold stress memory, highlighting a role for DNA methylation in preventing spurious gene activation and maintaining priming specificity. Notably, met1, deficient in CG methylation, shows reduced methylation at the CBF gene cluster, which correlates with its overexpression and enhanced activation of downstream cold-responsive genes. Our findings demonstrate that DNA methylation modulates cold stress memory by shaping chromatin states and ensuring transcriptional precision.