Ecotype-specific sensitivity to DNA methylation inhibitors in Arabidopsis cmt3 mutants

DNA methylation inhibitors such as 5-aza-2'-deoxycytidine (5-Aza-2dC) are widely used to probe epigenetic regulation, yet genetic factors underlying natural variation in inhibitor sensitivity remain poorly understood. Here, we investigated ecotype-specific responses to 5-Aza-2dC in Arabidopsis thaliana, focusing on cmt3 mutants in the Columbia (Col-0) and Landsberg erecta (Ler) backgrounds. We found that cmt3 mutants displayed contrasting phenotypes depending on genetic background: Col-0 cmt3 mutants showed relative resistance to 5-Aza-2dC, whereas Ler cmt3 mutants exhibited pronounced sensitivity. Genetic analyses indicated that this enhanced sensitivity in the Ler background is recessive and cannot be explained solely by loss of CMT3 function. Through genetic mapping, we identified At1g34770 (NSE3) as a strong candidate modifier associated with 5-Aza-2dC sensitivity. A non-synonymous substitution in NSE3 correlated with growth inhibition under inhibitor treatment, and transgenic analyses further supported a contributory role for this gene. Together, our results demonstrate that natural genetic modifiers, including allelic variation in NSE3, shape ecotype-dependent responses to DNA methylation inhibition, highlighting the importance of genetic background in modulating epigenetic perturbations in plants.