Development of a new strategy to control gene expression by chromatin conversion

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DNA methylation contributes to genome regulation including control of gene transcription and chromatin structure. Normally, methylation occurs at position 5 of cytosine within CpG dinudeotides, which implicates the formation of transcriptionally inactive chromatin. In the nucleus, not only is the DNA methylated, but the methylated DNA must also be interpreted by methyl-CpG binding domain proteins (MBD proteins). There are at least five mammalian MBD proteins: MeCP2, MBD1, MBD2, MBD3, and MBD4 (also known as MED1).Recently, we have presented evidence that MBD1 acts as a transcriptional regulator through the cooperation of MBD, cysteine-rich CXXC domains, and a C-terminal transcriptional repression domain (TRD). Further, we have determined the structure of the MBD from MBD1 in complex with methylated DNA by multi-dimensional heteronudear NMR spectroscopy. Mutant-types MBD in which the functionally important residues Arg22, Arg30, Asp32, Tyr34, Arg44, Ser45 and Tyr52 were changed to alanine lost the ability to bind methylated DNA. Although MeCP2, MBD2, and MBD3 are embedded in the histone deacetylase complexes, MBD1 has not been found in known histone deacetylase complexes, suggesting that MBD1 may form a novel represser complex or chromatin. To inhibit gene expression in vivo, we have developed some newly designed molecules containing a DNA binding domain of certain transcription factor and the TRD of MBD1 or MeCP2. Because the MBD mutants can reverse methylation-dependet gene silencing, these molecules seem to be useful for reactivating the repressed genes. Based on our findings we provide a mechanistic basis for gene silencing in methylation-dependent manners and a new tool to control gene expression.