Abstract
Unlike other members of the methyl-cytosine binding domain (MBD) family, MBD4 serves as a potent DNA glycosylase in DNA mismatch repair specifically targeting mCpG/TpG mismatches arising from spontaneous deamination of methyl-cytosine. The protein contains an N-terminal MBD (MBD4MBD) and a C-terminal glycosylase domain (MBD4GD) separated by a long linker. This arrangement suggests that the MBD4MBD either directly augments enzymatic catalysis by the MBD4GD or targets the protein to regions enriched for mCpG/TpG mismatches. Here we present structural and dynamic studies of MBD4MBD bound to dsDNA. We show that MBD4MBD binds with a modest preference formCpG as compared to mismatch, unmethylated and hydroxymethylated DNA. We find that while MBD4MBD exhibits slow exchange between molecules of DNA (intermolecular exchange), the domain exhibits fast exchange between two sites in the same molecule of dsDNA (intramolecular exchange). Introducing a single-strand defect between binding sites does not greatly reduce the intramolecular exchange rate, consistent with a local hopping mechanism for moving along the DNA. These results support a model in which the MBD4MBD4 targets the intact protein to mCpG islands and promotes scanning by rapidly exchanging between successive mCpG sites which facilitates repair of nearby mCpG/TpG mismatches by the glycosylase domain.
Highlights
DNA methylation involves enzymatic addition of a methyl group at the C5 position of the symmetrically opposed cytosine bases in a double stranded cytosine-guanosine sequence (CpG) and serves as a key epigenetic signal in developmental and tissue type specific regulatory mechanisms such as gene silencing, chromatin modifications and aberrant silencing of tumor suppressor genes in cancer [1]
MBD4 represents a unique member of the methyl-cytosine binding domain (MBD) family in that it contains intrinsic enzymatic activity provided by a C-terminal glycosylase domain (MBD4GD) in addition to an N-terminal MBD (MBD4MBD)
Nucleic Acids Research, 2014, Vol 42, No 17 11219 ternatively the MBD4MBD could target the protein to regions enriched for mCpG sites and allow the MBD4GD to repair mismatches at nearby sites [4]
Summary
DNA methylation involves enzymatic addition of a methyl group at the C5 position of the symmetrically opposed cytosine bases in a double stranded cytosine-guanosine sequence (CpG) and serves as a key epigenetic signal in developmental and tissue type specific regulatory mechanisms such as gene silencing, chromatin modifications and aberrant silencing of tumor suppressor genes in cancer [1]. Central to these regulatory functions is a family of proteins that selectively bind symmetrically methylated CG dinucleotide sequences (mCpG) through a common methyl-cytosine binding domain (MBD). The mCpG/TpG (or mCpG/hmUpG) mismatch arises from hydrolytic deamination of a methyl-cytosine (or hydroxymethylcytosine) to thymine (or hydroxmethyluracil) and represents one of the more common sources of germ line and somatic DNA point mutations
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