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The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites

A Corrigendum to this article was published on 30 March 2000

Abstract

In addition to its well-documented effects on gene silencing, cytosine methylation is a prominent cause of mutations. In humans, the mutation rate from 5-methylcytosine (m5C) to thymine (T) is 10–50-fold higher1,2,3,4 than other transitions and the methylated sequence CpG is consequently under-represented5. Over one-third of germline point mutations associated with human genetic disease6 and many somatic mutations leading to cancer7,8 involve loss of CpG. The primary cause of mutability appears to be hydrolytic deamination. Cytosine deamination produces mismatched uracil (U), which can be removed by uracil glycosylase9,10, whereas m5C deamination generates a G·T mispair that cannot be processed by this enzyme. Correction of m5CpG·TpG mismatches may instead be initiated by the thymine DNA glycosylase, TDG11,12. Here we show that MBD4, an unrelated mammalian protein that contains a methyl-CpG binding domain13,14, can also efficiently remove thymine or uracil from a mismatches CpG site in vitro. Furthermore, the methyl-CpG binding domain of MBD4 binds preferentially to m5CpG·TpG mismatches—the primary product of deamination at methyl-CpG. The combined specificities of binding and catalysis indicate that this enzyme may function to minimize mutation at methyl-CpG.

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Figure 1: MBD4 contains a conserved glycosylase-like domain and a methyl-CpG-binding domain.
Figure 2: MBD4 is a mismatch-specific T/U DNA glycosylase.
Figure 3: DNA-binding specificities of MBD4 and its truncated derivatives to DNA containing methylated and non-methylated duplexes with or without G·U or G·T mismatches.
Figure 4: The properties of MBD4 suggest a role in initiating repair of m5CpG·TpG mismatches.

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Acknowledgements

We thank P. Hunziger for HPLC analysis; P. Schär, R. Wood and T. Lindahl for fruitful discussions; I. Hickson for the HAP1 endonuclease; and S. Tweedie for comments on the manuscript. This work was supported by grants from the Wellcome Trust (B.H. and A.B.), the Schweizerische Krebsliga (U.H. and J.J.) and by a Darwin Trust Scholarship to H-H.N.

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Correspondence to Adrian Bird.

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Hendrich, B., Hardeland, U., Ng, HH. et al. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 401, 301–304 (1999). https://doi.org/10.1038/45843

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