DNA methylome responses to biotic and abiotic stress in Arabidopsis thaliana: A multi-study analysis

Abstract

Plants have evolved complex physiological and morphological strategies to cope with biotic and abiotic stress. At the molecular level, these responses are partly mediated by epigenetic mechanisms such as DNA methylation. In Arabidopsis thaliana, numerous studies have examined stress-induced changes in DNA methylation, aiming to elucidate their roles in stress acclimation. However, comparing these studies remains difficult due to variations in analytical methods and focus. To address this, we conducted an integrative analysis of 13 studies (16 datasets) using a unified bioinformatic pipeline to identify common and stress-specific methylation responses. Our results show that the number and distribution of differentially methylated regions (DMRs) vary by stress type and methylation context CG, CHG, and CHH. CG DMRs were primarily located in gene bodies, while CHG and CHH DMRs were enriched in transposable elements (TEs). Gene Ontology analysis revealed consistently enriched stress-related terms across conditions, indicating shared epigenetic regulation. As TEs have been proposed to act as stress sensors and regulators of nearby gene expression, we examined gene-proximal TEs in more detail. We found significant enrichment of stress-responsive methylation changes in LINE/L1, RathE1_ons, and DNA/HAT elements. While stress-induced methylation is often considered transient, many affected CG DMRs overlapped with loci known to accumulate stable epimutations over generations, suggesting that stress may contribute to long-term heritable epigenetic variation. These findings enhance our understanding of epigenetic regulation in plant stress responses, highlighting both shared and stress-specific methylation dynamics. Significance statementWe combined 16 Arabidopsis thaliana Whole-Genome Bisulfite Sequencing datasets to reveal common and stress-specific DNA methylation responses. Although global methylation levels remained stable, specific DMRs varied according to the type of stress and genomics context. Gene Ontology analysis revealed shared stress pathways. Gene-proximal transposable elements (TEs) (e.g. LINE/L1, RathE1_ons, DNA/HAT) were enriched for stress-responsive methylation changes. Notably, a subset of stress-induced CG DMRs overlap with epimutation-prone loci, suggesting an environmental route toward stable, heritable epigenetic variation.