The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites (original) (raw)

Nature volume 401, pages 301–304 (1999)Cite this article

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.

This is a preview of subscription content, access via your institution

Access options

Subscribe to this journal

Receive 51 print issues and online access

$199.00 per year

only $3.90 per issue

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Additional access options:

Similar content being viewed by others

References

  1. Duncan,B. K. & Miller,J. H. Mutagenic deamination of cytosine residues in DNA. Nature 287, 560– 561 (1980).
    Article ADS CAS Google Scholar
  2. Britten,R. J., Baron,W. F., Stout,D. B. & Davidson,E. H. Sources and evolution of human Alu repeated sequences. Proc. Natl Acad. Sci. USA 85, 4770–4774 ( 1988).
    Article ADS CAS Google Scholar
  3. Sved,J. & Bird,A. The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc. Natl Acad. Sci. USA 87, 4692–4696 (1990).
    Article ADS CAS Google Scholar
  4. Bulmer,M. Neighboring base effects on substitution rates in pseudogenes. Mol. Biol. Evol. 3, 322–329 (1986).
    CAS PubMed Google Scholar
  5. Bird,A. P. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res. 8, 1499–1594 (1980).
    Article CAS Google Scholar
  6. Cooper,D. N. & Youssoufian,H. The CpG dinucleotide and human genetic disease. Hum. Genet. 78, 151– 15 (1988).
    Article CAS Google Scholar
  7. Hollstein,M. et al. Database of p53 gene somatic mutations in human tumors and cell lines. Nucleic Acids Res. 22, 3551– 3555 (1994).
    CAS PubMed PubMed Central Google Scholar
  8. Jones,P. A., Rideout,W. M., Shen, J.-C., Spruck,C. H. & Tsai,Y. C. Methylation, mutation and cancer. BioEssays 14, 33–36 ( 1992).
    Article CAS Google Scholar
  9. Lindahl,T. An N-glycosidase from Escherichia coli that releases free uracil from DNA containing deaminated cytosine residues. Proc. Natl Acad. Sci. USA 71, 3649–3653 ( 1974).
    Article ADS CAS Google Scholar
  10. Lindahl,T., Karran,P. & Wood,R. D. DNA excision repair pathways. Curr. Opin. Genet. Dev. 7, 158–169 ( 1997).
    Article CAS Google Scholar
  11. Wiebauer,K. & Jiricny,J. In vitro correction of G·T mispairs to G·C pairs in nuclear extracts from human cells. Nature 339, 234–236 ( 1989).
    Article ADS CAS Google Scholar
  12. Neddermann,P. et al. Cloning and expression of human G/T mismatch-specific thymine-DNA glycosylase. J. Biol. Chem. 271, 12767– 12774 (1996).
    Article CAS Google Scholar
  13. Nan,X., Meehan,R. R. & Bird,A. Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. Nucleic Acids Res. 21, 4886 –4892 (1993).
    Article CAS Google Scholar
  14. Hendrich,B. & Bird,A. Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol. Cell. Biol. 18, 6538–6547 ( 1998).
    Article CAS Google Scholar
  15. Nan,X., Campoy,J. & Bird,A. MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin. Cell 88, 471– 481 (1997).
    Article CAS Google Scholar
  16. Michaels,M. L., Pham,L., Nghiem,M., Cruz,C. & Miller,J. H. MutY, an adenine glycosylase active on G-A mispairs, has homology to endonuclease III. Nucleic Acids Res. 18 , 3841–3845 (1990).
    Article CAS Google Scholar
  17. Horst,J. P. & Fritz,H. J. Counteracting the mutagenic effect of hydrolytic deamination of DNA 5-methylcytosine residues at high temperature: DNA mismatch N-glycosylase Mig.Mth of the thermophilic archaeon Methanobacterium thermoactotrophicum THF. EMBO J. 15, 5459–5469 (1996).
    Article CAS Google Scholar
  18. Asahara,H., Wistort,P. M., Bank,J. F., Bakerian,R. H. & Cunningham,R. P. Purification and characterization of Escherichia coli endonuclease III from the cloned nth gene. Biochemistry 28, 444–4449 (1989).
    Article Google Scholar
  19. Shiota,S. & Nakayama,H. UV endonuclease of Micrococcus luteus, a cyclobutane pyrimidine dimer-DNA glycosylase/abasic lyase: cloning and characterization of the gene. Proc. Natl Acad. Sci. USA 94, 593–598 (1997).
    Article ADS CAS Google Scholar
  20. Robson,C. N. & Hickson,I. D. Isolation of cDNA clones encoding a human apurinic/apyrimidinic endonuclease that corrects DNA repair and mutagenesis defects in E. coli xth (exonuclease III) mutants. Nucleic Acids Res. 19, 5519–5523 (1991).
    Article CAS Google Scholar
  21. Scharer,O. D., Nash,H. M., Jiricny,J., Laval,J. & Verdine,G. L. Specific binding of a designed pyrrolidine abasic site analog to multiple DNA glycosylases. J. Biol. Chem. 273, 8592–8597 (1998).
    Article CAS Google Scholar
  22. Gallinari,P. & Jiricny,J. A new class of uracil-DNA glycosylases related to human thymine-DNA glycosylase. Nature 383 , 735–738 (1996).
    Article ADS CAS Google Scholar
  23. Sibghat-Ullah et al. Base analog and neighboring base effects on substrate specificity of recombinant human G:T mismatch-specific thymine DNA glycosylase. Biochemistry 35, 12926–12932 ( 1996).
    Article CAS Google Scholar
  24. Bellacosa,A. et al. MED1, a novel human methyl-CpG-binding endonuclease, interacts with DNA mismatch repair protein MLH1. Proc. Natl Acad. Sci. USA 96, 3969–3974 ( 1999).
    Article ADS CAS Google Scholar
  25. Modrich,P. & Lahue,R. Mismatch repair in replication fidelity, genetic recombination and cancer biology. Annu. Rev. Biochem. 65, 101–133 (1996).
    Article CAS Google Scholar
  26. Jiricny,J. Replication errors: cha(lle)nging the genome. EMBO J. 17, 6427–6436 (1998).
    Article CAS Google Scholar
  27. Maniatis,T., Fritsch,E. F. & Sambrook, J. Molecular Cloning: A Laboratory Manual 196 –198 (Cold Spring Harbor, New York, 1982).

Download references

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.

Author information

Author notes

  1. Brian Hendrich, Ulrike Hardeland and Josef Jiricny: These authors contributed equally to this work.

Authors and Affiliations

  1. Institute of Cell and Molecular Biology, University of Edinburgh, The King's Buildings, Mayfield Road, Edinburgh, EH9 3JR, UK
    Brian Hendrich, Huck-Hui Ng & Adrian Bird
  2. Institute of Medical Radiobiology , August Forel-Strasse 7, Zürich, CH-8008, Switzerland
    Ulrike Hardeland & Josef Jiricny

Authors

  1. Brian Hendrich
    You can also search for this author inPubMed Google Scholar
  2. Ulrike Hardeland
    You can also search for this author inPubMed Google Scholar
  3. Huck-Hui Ng
    You can also search for this author inPubMed Google Scholar
  4. Josef Jiricny
    You can also search for this author inPubMed Google Scholar
  5. Adrian Bird
    You can also search for this author inPubMed Google Scholar

Corresponding author

Correspondence toAdrian Bird.

Rights and permissions

About this article

Cite this article

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

Download citation