The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA (original) (raw)

Nature volume 450, pages 908–912 (2007)Cite this article

Abstract

DNA methyltransferase (cytosine-5) 1 (Dnmt1) is the principal enzyme responsible for maintenance of CpG methylation and is essential for the regulation of gene expression, silencing of parasitic DNA elements, genomic imprinting and embryogenesis1,2,3,4. Dnmt1 is needed in S phase to methylate newly replicated CpGs occurring opposite methylated ones on the mother strand of the DNA, which is essential for the epigenetic inheritance of methylation patterns in the genome. Despite an intrinsic affinity of Dnmt1 for such hemi-methylated DNA5, the molecular mechanisms that ensure the correct loading of Dnmt1 onto newly replicated DNA in vivo are not understood. The Np95 (also known as Uhrf1 and ICBP90) protein binds methylated CpG through its SET and RING finger-associated (SRA) domain6. Here we show that localization of mouse Np95 to replicating heterochromatin is dependent on the presence of hemi-methylated DNA. Np95 forms complexes with Dnmt1 and mediates the loading of Dnmt1 to replicating heterochromatic regions. By using Np95-deficient embryonic stem cells and embryos, we show that Np95 is essential in vivo to maintain global and local DNA methylation and to repress transcription of retrotransposons and imprinted genes. The link between hemi-methylated DNA, Np95 and Dnmt1 thus establishes key steps of the mechanism for epigenetic inheritance of DNA methylation.

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References

  1. Li, E., Bestor, T. H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992)
    Article CAS PubMed Google Scholar
  2. Li, E., Beard, C. & Jaenisch, R. Role for DNA methylation in genomic imprinting. Nature 366, 362–365 (1993)
    Article ADS CAS PubMed Google Scholar
  3. Jackson-Grusby, L. et al. Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation. Nature Genet. 27, 31–39 (2001)
    Article CAS PubMed Google Scholar
  4. Walsh, C. P., Chaillet, J. R. & Bestor, T. H. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nature Genet. 20, 116–117 (1998)
    Article CAS PubMed Google Scholar
  5. Fatemi, M., Hermann, A., Pradhan, S. & Jeltsch, A. The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA. J. Mol. Biol. 309, 1189–1199 (2001)
    Article CAS PubMed Google Scholar
  6. Unoki, M., Nishidate, T. & Nakamura, Y. ICBP90, an E2F-1 target, recruits HDAC1 and binds to methyl-CpG through its SRA domain. Oncogene 23, 7601–7610 (2004)
    Article CAS PubMed Google Scholar
  7. Klose, R. J. & Bird, A. P. Genomic DNA methylation: the mark and its mediators. Trends Biochem. Sci. 31, 89–97 (2006)
    Article CAS PubMed Google Scholar
  8. Goll, M. G. & Bestor, T. H. Eukaryotic cytosine methyltransferases. Annu. Rev. Biochem. 74, 481–514 (2005)
    Article CAS PubMed Google Scholar
  9. Chuang, L. S. et al. Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21WAF1. Science 277, 1996–2000 (1997)
    Article CAS PubMed Google Scholar
  10. Spada, F. et al. DNMT1 but not its interaction with the replication machinery is required for maintenance of DNA methylation in human cells. J. Cell Biol. 176, 565–571 (2007)
    Article CAS PubMed PubMed Central Google Scholar
  11. Woo, H. R., Pontes, O., Pikaard, C. S. & Richards, E. J. VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization. Genes Dev. 21, 267–277 (2007)
    Article CAS PubMed PubMed Central Google Scholar
  12. Bonapace, I. M. et al. Np95 is regulated by E1A during mitotic reactivation of terminally differentiated cells and is essential for S phase entry. J. Cell Biol. 157, 909–914 (2002)
    Article CAS PubMed PubMed Central Google Scholar
  13. Muto, M. et al. Targeted disruption of Np95 gene renders murine embryonic stem cells hypersensitive to DNA damaging agents and DNA replication blocks. J. Biol. Chem. 277, 34549–34555 (2002)
    Article CAS PubMed Google Scholar
  14. Papait, R. et al. Np95 is implicated in pericentromeric heterochromatin replication and in major satellite silencing. Mol. Biol. Cell 18, 1098–1106 (2007)
    Article CAS PubMed PubMed Central Google Scholar
  15. de Boer, E. et al. Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc. Natl Acad. Sci. USA 100, 7480–7485 (2003)
    Article ADS CAS PubMed PubMed Central Google Scholar
  16. Suetake, I., Miyazaki, J., Murakami, C., Takeshima, H. & Tajima, S. Distinct enzymatic properties of recombinant mouse DNA methyltransferases Dnmt3a and Dnmt3b. J. Biochem. 133, 737–744 (2003)
    Article CAS PubMed Google Scholar
  17. Leonhardt, H., Page, A. W., Weier, H. U. & Bestor, T. H. A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei. Cell 71, 865–873 (1992)
    Article CAS PubMed Google Scholar
  18. Okano, M., Bell, D. W., Haber, D. A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999)
    Article CAS PubMed Google Scholar
  19. Tsumura, A. et al. Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells 11, 805–814 (2006)
    Article CAS PubMed Google Scholar
  20. Bachman, K. E., Rountree, M. R. & Baylin, S. B. Dnmt3a and Dnmt3b are transcriptional repressors that exhibit unique localization properties to heterochromatin. J. Biol. Chem. 276, 32282–32287 (2001)
    Article CAS PubMed Google Scholar
  21. Lin, I. G. et al. Murine de novo methyltransferase Dnmt3a demonstrates strand asymmetry and site preference in the methylation of DNA in vitro . Mol. Cell. Biol. 22, 704–723 (2002)
    Article CAS PubMed PubMed Central Google Scholar
  22. Chen, T. et al. Complete inactivation of DNMT1 leads to mitotic catastrophe in human cancer cells. Nature Genet. 39, 391–396 (2007)
    Article CAS PubMed Google Scholar
  23. Takebayashi, S., Tamura, T., Matsuoka, C. & Okano, M. Major and essential role for DNA methylation mark in mouse embryogenesis and stable association of DNMT1 with newly replicated regions. Mol. Cell. Biol. 27, 8243–8258 (2007)
    Article CAS PubMed PubMed Central Google Scholar
  24. Bostick, M. et al. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 317, 1760–1764 (2007)
    Article ADS CAS PubMed Google Scholar
  25. Damelin, M. & Bestor, T. H. Biological functions of DNA methyltransferase 1 require its methyltransferase activity. Mol. Cell. Biol. 27, 3891–3899 (2007)
    Article CAS PubMed PubMed Central Google Scholar
  26. Pradhan, S. & Kim, G. D. The retinoblastoma gene product interacts with maintenance human DNA (cytosine-5) methyltransferase and modulates its activity. EMBO J. 21, 779–788 (2002)
    Article CAS PubMed PubMed Central Google Scholar
  27. Reale, A. et al. Modulation of DNMT1 activity by ADP-ribose polymers. Oncogene 24, 13–19 (2005)
    Article CAS PubMed Google Scholar
  28. Estève, P. O. et al. Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication. Genes Dev. 20, 3089–3103 (2006)
    Article PubMed PubMed Central Google Scholar
  29. Carlone, D. L. et al. Reduced genomic cytosine methylation and defective cellular differentiation in embryonic stem cells lacking CpG binding protein. Mol. Cell. Biol. 25, 4881–4891 (2005)
    Article CAS PubMed PubMed Central Google Scholar
  30. Koberna, K. et al. Nuclear organization studied with the help of a hypotonic shift: its use permits hydrophilic molecules to enter into living cells. Chromosoma 108, 325–335 (1999)
    Article CAS PubMed Google Scholar

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Acknowledgements

This work was supported in part by a grant from the Genome Network Project (to H.K.), by the ‘Ground-based Research Program for Space Utilization’ promoted by the Japan Space Forum (H.K.) and by a grant-in-aid for Scientific Research on Priority Areas (germ-cell development, reprogramming and epigenetics, to M.O. and K.M.) from the Ministry of Education, Culture, Sports, Science and Technology, Japan. We thank W. Reik, N. Brockdorff, P. Burrows, H. Niwa, H. Sano, J. Strouboulis and M. Vidal for critical reading and reagents.

Author Contributions J. Sharif., K.O. and K.M. performed DNA methylation and gene expression analyses; M.M., Y.M.-K. and H.K. generated, maintained and performed phenotypic analyses of knockout mice; M.M., J. Shinga. and A.I. purified the protein complexes and performed mass spectrometry analyses; S. Takebayashi and M.O. performed immunofluorescence analysis; M.M., I.S. and S. Tajima performed the DNA methylation assay; and T.A.E. and T.T. performed statistical analyses. K.M., M.O. and H.K. designed the study, wrote the paper and contributed equally as co-senior authors. All authors discussed the results and commented on the manuscript.

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Author notes

  1. Jafar Sharif, Masahiro Muto and Shin-ichiro Takebayashi: These authors contributed equally to this work.

Authors and Affiliations

  1. Tohoku University Biomedical Engineering Research Organization (TUBERO), 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan ,
    Jafar Sharif & Kohzoh Mitsuya
  2. Department of Obstetrics and Gynecology, Tohoku University School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan,
    Jafar Sharif & Kunihiro Okamura
  3. Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan,
    Jafar Sharif
  4. RIKEN Research Center for Allergy and Immunology,,
    Masahiro Muto, Jun Shinga, Yoko Mizutani-Koseki & Haruhiko Koseki
  5. RIKEN Genomic Sciences Center, 1-7-22 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan ,
    Takaho A. Endo & Tetsuro Toyoda
  6. RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan ,
    Shin-ichiro Takebayashi & Masaki Okano
  7. Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan ,
    Isao Suetake & Shoji Tajima
  8. Protein-Research Network, Inc., 1-13-5 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan ,
    Akihiro Iwamatsu

Authors

  1. Jafar Sharif
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  2. Masahiro Muto
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  3. Shin-ichiro Takebayashi
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  4. Isao Suetake
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  5. Akihiro Iwamatsu
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  6. Takaho A. Endo
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  7. Jun Shinga
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  8. Yoko Mizutani-Koseki
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  9. Tetsuro Toyoda
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  10. Kunihiro Okamura
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  11. Shoji Tajima
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  12. Kohzoh Mitsuya
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  13. Masaki Okano
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  14. Haruhiko Koseki
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Corresponding author

Correspondence toHaruhiko Koseki.

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Supplementary information

Supplementary Information

The file contains Supplementary Figures S1-S8 with Legends and Supplementary Tables 1-3. This document shows biochemical properties of NP95 complexes, supplementary evidences for recognition of hemi-methylated DNA by Np95, generation and phenotypes of Np95-deficient mice, normal expression of Dnmt3a and -3b and cell-cycle progression in Np95-deficient ES cells and others. (PDF 776 kb)

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Sharif, J., Muto, M., Takebayashi, Si. et al. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA.Nature 450, 908–912 (2007). https://doi.org/10.1038/nature06397

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