Plant-specific function of H3K9me3 as a permissive chromatin mark during Arabidopsis seed germination

Seed dormancy and germination are sequential phases, both tightly regulated by environmental and hormonal cues to ensure germination under favorable conditions. While hormonal and transcriptional regulators are well characterized, the epigenetic mechanisms governing these transitions are less understood. We profiled H3K4me3, H3K27me3, and H3K9me3 in the seeds of Arabidopsis thaliana Columbia-0 and Cape Verde Islands, representing shallow and deep dormancy, respectively, at freshly harvested (FH), after-ripened (AR), and germination-stimulated (GS) states. H3K4me3 and H3K9me3 co-localized in euchromatic, transcriptionally active regions, whereas H3K27me3 occupied repressive domains. Histone methylation landscapes were stable from FH to AR but showed a marked H3K9me3 increase from AR to GS in association with the activation of genes related to translation, energy metabolism, and cell division. Co-marking by H3K4me3 and H3K9me3 correlated with highest transcript levels. During dormancy release, AR-repressed genes, including DOG1 , showed targeted reductions in H3K4me3 and H3K9me3 levels. These findings support a plant-specific role of H3K9me3 as an active or permissive chromatin mark promoting transcriptional reprogramming during germination.