DDM1-Mediated DNA Methylation Regulates Leaf Serration in Arabidopsis thaliana

DNA methylation is a crucial epigenetic modification that is stably inherited across both mitotic and meiotic cell divisions in plants. It is regulated by multiple epigenetic pathways, and alterations in methylation can lead to phenotypic variation independent of changes in the DNA sequence. In this study, changes in DNA methylation triggered by the chromatin remodeler DDM1 (DECREASE IN DNA METHYLATION 1) were found to influence leaf phenotypes in Arabidopsis thaliana. The ddm1 mutation dramatically reduced genome-wide DNA methylation, particularly in transposable elements (TEs). Hypomethylation of TEs activated downstream genes, including DPA4 (DEVELOPMENT-RELATED PCG TARGET IN THE APEX 4), which suppresses CUC2 (CUP-SHAPED COTYLEDON 2), a key regulator of leaf serration. Importantly, methylation changes in the DPA4 promoter were stably inherited in the F₂ generation. This study identified DPA4 as a gene affected by the ddm1 mutation, which significantly affects leaf serration in A. thaliana. These findings highlight the impact of induced epigenetic modifications on plant development, providing a basis for further exploration of heritable epigenetic traits.