RNA sequencing (RNA-seq) of primed and non-primed Arabidopsis thaliana under cold-stress
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. In this study, we investigated transcriptomic and DNA methylation dynamics in cold-primed and non-primed Arabidopsis thaliana plants. 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). Notably, CHH methylation within gene bodies and TEs is markedly reduced in cold-primed plants, suggesting a role for DNA hypomethylation in establishing cold stress memory. This hypomethylation correlates with decreased expression of the CMT2 DNA methyltransferase and components of the RNA-directed DNA methylation (RdDM) pathway, indicating a passive demethylation process during cold treatment. Furthermore, DNA methylation mutants exhibit enhanced cold stress memory, highlighting the role of methylation in preventing spurious gene activation and maintaining priming specificity. Particularly, met1, deficient in CG methylation, shows reduced methylation at the CBF gene cluster, correlating with their overexpression and enhanced activation of downstream cold-responsive genes. Our findings show that DNA methylation modulates cold stress memory by shaping chromatin and ensuring transcriptional precision.
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. In this study, we investigated transcriptomic and DNA methylation dynamics in cold-primed and non-primed Arabidopsis thaliana plants. 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). Notably, CHH methylation within gene bodies and TEs is markedly reduced in cold-primed plants, suggesting a role for DNA hypomethylation in establishing cold stress memory. This hypomethylation correlates with decreased expression of the CMT2 DNA methyltransferase and components of the RNA-directed DNA methylation (RdDM) pathway, indicating a passive demethylation process during cold treatment. Furthermore, DNA methylation mutants exhibit enhanced cold stress memory, highlighting the role of methylation in preventing spurious gene activation and maintaining priming specificity. Particularly, met1, deficient in CG methylation, shows reduced methylation at the CBF gene cluster, correlating with their overexpression and enhanced activation of downstream cold-responsive genes. Our findings show that DNA methylation modulates cold stress memory by shaping chromatin and ensuring transcriptional precision.
European Bioinformatics Institute