DNA Methylation Fine-Tunes Light- and Hormone-Responsive Growth Plasticity in Arabidopsis Seedlings

DNA methylation regulates plant growth by modulating gene expression; however, its contribution to hormone responsiveness and photomorphogenesis remains only partially understood. We examined <i>Arabidopsis thaliana</i> DNA methylation mutants <i>met1</i> and <i>drm1</i>, <i>drm2</i>, and <i>cmt3</i> (<i>ddc</i>) under defined light regimes and following exogenous treatments with auxin, gibberellin, and the auxin transport inhibitor TIBA. Hypocotyl elongation and cotyledon expansion exhibited strong light dependency across all genotypes, with <i>met1</i> seedlings developing a consistently reduced cotyledon area and <i>ddc</i> seedlings displaying impaired hypocotyl elongation under specific light qualities. Exogenous auxin inhibited growth in all genotypes, whereas GA₃ promoted elongation in hypocotyls and roots (by approximately 75-80% and 15-35%, respectively, in Col0 and <i>met1</i>), with <i>ddc</i> exhibiting delayed and non-linear dose-dependent sensitivity. Quantitative RT-PCR analysis revealed differential expression of genes involved in auxin transport (<i>PIN1</i>, <i>PIN3</i>, <i>PIN7</i>), auxin signalling (<i>ARF7</i>, <i>IAA3</i>, <i>LAX3</i>), circadian regulation (<i>TOC1</i>, <i>LHY</i>, <i>CCA1</i>), and light signalling (<i>PIFs</i>, <i>HY5</i>, <i>HYH</i>), supporting a link between DNA methylation status and coordinated regulation of hormone-, light-, and clock-controlled transcriptional networks. Together, these findings demonstrate that MET1- and DRM/CMT-dependent methylation pathways integrate epigenetic regulation with environmental and hormonal cues, modulating the intensity, timing, and organ specificity of growth responses, thereby fine-tuning growth plasticity during early <i>Arabidopsis</i> seedling development.