The MdSUVH–MdDNAJ complex binds to methylated MITE-MdRF1 and activates MdRFNR1-1 expression in response to drought stress. A, Binding of MdSUVH1 and MdSUVH3 to methylated MITE-MdRF1 in the MdRFNR1-1 promoter, as revealed by DAP-qPCR. DAP, methylated DNA library. Amp-DAP, amplified DNA library, which contained non-methylated DNA. WT, wild type; M, mutant version of MdSUVH1 or MdSUVH3, in which Tyr290 of MdSUVH1 was mutated to Ala290 and Tyr317 of MdSUVH3 was mutated to Ala317. Error bars indicate sd, n = 3. B and C, Relative luciferase activity from the dual luciferase reporter assays in N. benthamiana leaves. Quantification was performed by normalizing firefly luciferase activity to that of Renilla luciferase, 35S:REN was used as an internal control. Error bars indicate se, n = 8. Statistical analyses were performed by the Student’s t test and statistically significant differences are indicated by *P ≤ 0.05, **P ≤ 0.01, or ***P ≤ 0.001. ns, no significant difference.