SHH1 cooperates with the DNA methylation reader MBD7 to suppress transcriptional silencing of promoter-methylated genes in Arabidopsis

In Arabidopsis thaliana, METHYL-CpG-BINDING DOMAIN 7 (MBD7) and its associated α-crystallin domain (ACD) proteins form a complex that interprets DNA methylation to prevent the silencing of methylated luciferase (LUC) reporter transgenes. However, the mechanism by which the MBD7 complex effectively targets methylated transgenes remains largely unclear. Here, we identify a novel role for SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1), extending its function beyond the canonical RNA-directed DNA methylation (RdDM) pathway. We demonstrate that SHH1 prevents the transcriptional silencing of methylated LUC transgenes and a subset of endogenous genes by acting in concert with MBD7 within the same regulatory pathway. SHH1 co-localizes with MBD7 at nuclear foci and physically interacts with it to enhance its stability. Furthermore, SHH1 binds to methylated loci via its SAWADEE domain, which recognizes the H3K9me2 histone mark. This interaction promotes the reciprocal recruitment of SHH1 and MBD7 to methylated loci, revealing a cooperative mechanism that maintains transcriptional activity at promoter-methylated genes. Collectively, our findings unveil a dynamic, mutually reinforcing SHH1-MBD7 module that enhances the expression of promoter-methylated genes, likely by facilitating effective binding to chromatin marked by repressive epigenetic modifications. This work provides important insights into how DNA methylation fine-tunes gene expression in plants by balancing between transcriptional repression and activation.