Carbon dots - driven epigenome reprogramming reshapes DNA methylation landscapes in rice

DNA methylation plays a crucial role in the regulation of gene expression, ensuring normal growth and development and enabling responses to biotic and abiotic stresses in plants. Carbon dots (CDs) can participate in the entire plant life cycle and improve yield, however, the understanding of how CDs affect plant growth remains limited. Here, we demonstrate that CDs induce subtle but significant global DNA hypermethylation in rice, particularly in CHG and CHH contexts. This hypermethylation may be driven by the upregulation of OsCMTs triggered by CDs. CDs can stabilize i-motifs—potential regulators of active genes—in the promoter regions of OsCMT1 and OsCMT2, leading to increased CHG and CHH methylation. Our findings suggest that CDs modulate global DNA methylation changes, influencing the transcription of genes associated with phenotypic alterations in plants.