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

Plants experience diverse biotic and abiotic stresses that can induce changes in DNA methylation. However, comparisons among existing studies are complicated by differences in analytical methods and experimental designs. We aimed to identify shared and stress-specific DNA methylation responses across studies.

We reanalysed 16 whole-genome bisulphite sequencing datasets from 13 Arabidopsis thaliana studies using a unified bioinformatics pipeline. Differentially methylated regions (DMRs) were assessed in the CG, CHG and CHH contexts and examined in relation to genes, transposable elements (TEs), Gene Ontology terms, gene-proximal TE superfamilies and epimutation-prone loci.

Global methylation levels were generally stable, whereas the number and genomic distribution of DMRs varied according to stress type and methylation context. CG-DMRs occurred primarily in gene bodies, while CHG- and CHH-DMRs were enriched in TEs. Functional analysis identified shared stress-related processes across conditions. Gene-proximal LINE/L1, RathE1_cons and DNA/HAT elements were enriched for stress-responsive methylation changes. A subset of stress-associated CG-DMRs overlapped loci known to accumulate stable epimutations over generations.

Standardized cross-study analysis revealed both shared and stress-specific methylation patterns. The association of stress-responsive DMRs with gene-proximal TEs and epimutation-prone loci suggests potential links among environmental responses, genome regulation and long-term epigenetic variation.