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

In Arabidopsis thaliana, the Methyl-CpG-Binding Domain 7 (MBD7) and its associated Alpha Crystallin Domain (ACD) proteins form a complex that interprets DNA methylation to prevent the silencing of methylated luciferase (LUC) reporter transgenes. However, how the MBD7 complex effectively targets methylated transgenes remains largely unclear. This study identifies 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 working in concert with MBD7, within the same regulatory pathway. SHH1 physically interacts with MBD7, co-localizes with it at nuclear foci, and enhances its stability. Furthermore, SHH1 binds to methylated loci through its SAWADEE domain, which recognizes the H3K9me2 histone mark. This interaction facilitates the recruitment of MBD7 to methylated loci and vice versa, revealing a cooperative mechanism between SHH1 and MBD7. Collectively, our findings unveil a dynamic, mutually reinforcing SHH1-MBD7 module that enhances the expression of promoter methylated genes, likely by promoting 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 coordinating the balance between transcriptional repression and activation.