DNA methylation contributes to plant acclimation to naturally fluctuating light

Summary Plants in the natural environment experience continuous dynamic changes in light intensity. Here, we exposed Arabidopsis thaliana plants to naturally fluctuating light (FL) regimes alongside traditional square light (SQ) regimes such as those often found in control environment growth chambers. The physiological response was highly consistent across experiments in sibling plants, indicating the possibility of an epigenetic mechanism, leading us to investigate differences in DNA methylation. Our results identified a large number of changes in DNA methylation patterns between FL‐acclimated plants and SQ‐acclimated plants, demonstrating that natural fluctuations in light impact plant epigenetic mechanisms. Most importantly, there are more differences in DNA methylation patterns between different light pattern regimes than between different light intensities. These differences in DNA methylation were accompanied by significant changes in gene expression, some of which correlated with altered DNA methylation. One of these genes, MCCA, was found to significantly impact photosynthetic efficiency when knocked out. Thousands of transposable element (TE) copies were differentially methylated between light regimes. Interestingly, up to 30% of these TEs are linked to nearby differentially expressed genes. Our data suggest DNA methylation plays a role in acclimation to natural light, which may directly regulate gene expression and impact TE activation.