DNA methylation is a highly conserved epigenetic modification associated with gene silencing in eukaryotic organisms. Extensive studies focused on the mechanisms by which DNA methylation is established and maintained have led to a quite detailed understanding of these pathways in both plants and mammals. However, how DNA methylation leads to gene silencing remains poorly understood. Candidates for facilitating DNA methylation-dependent gene silencing include proteins predicted to recognize methylated DNA, such as Methyl-DNA Binding Domain (MBD) proteins. In Arabidopsis, there are 13 such proteins, three of which (MBD5, MBD6 and MBD7) bind methylated DNA, in vitro, and localize to densely methylated, silent regions of the genome, in vivo. While these early studies are consistent with roles in gene silencing, the mechanisms through which these MBD proteins function remain unknown. To address this question, we employed a combination of biochemical and genetic approaches that led to the identification of a protein complex that regulates gene expression. This complex consists of two main components, MBD7 and a non-canonical heat stress protein, ACD51.9. Surprisingly, we found that this complex is required for promoting, rather than silencing, the expression of a methylated luciferase reporter construct. Furthermore, we find that the observed changes in gene expression occur without significantly altering the overall pattern of DNA methylation, suggesting that this complex regulates gene expression downstream of DNA methylation or via a novel pathway. As very few proteins have been characterized that function downstream of DNA methylation, further characterization of the MBD7-ACD51.9 complex offers as an entry point for understanding how DNA methylation affects gene expression.
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