Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism


DNA methylation of CpG dinucleotides is an important epigenetic modification of mammalian genomes and is essential for the regulation of chromatin structure, of gene expression and of genome stability1,2. Differences in DNA methylation patterns underlie a wide range of biological processes, such as genomic imprinting, inactivation of the X chromosome, embryogenesis, and carcinogenesis3,4,5,6. Inheritance of the epigenetic methylation pattern is mediated by the enzyme DNA methyltransferase 1 (Dnmt1), which methylates newly synthesized CpG sequences during DNA replication, depending on the methylation status of the template strands7,8. The protein UHRF1 (also known as Np95 and ICBP90) recognizes hemi-methylation sites via a SET and RING-associated (SRA) domain and directs Dnmt1 to these sites9,10,11. Here we report the crystal structures of the SRA domain in free and hemi-methylated DNA-bound states. The SRA domain folds into a globular structure with a basic concave surface formed by highly conserved residues. Binding of DNA to the concave surface causes a loop and an amino-terminal tail of the SRA domain to fold into DNA interfaces at the major and minor grooves of the methylation site. In contrast to fully methylated CpG sites recognized by the methyl-CpG-binding domain12,13, the methylcytosine base at the hemi-methylated site is flipped out of the DNA helix in the SRA–DNA complex and fits tightly into a protein pocket on the concave surface. The complex structure suggests that the successive flip out of the pre-existing methylated cytosine and the target cytosine to be methylated is associated with the coordinated transfer of the hemi-methylated CpG site from UHRF1 to Dnmt1.

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

Access options

Buy this article

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

Figure 1: Overall structure of the SRA domain.
Figure 2: Overall structure of the SRA–hemi-methylated CpG DNA complex.
Figure 3: Specific recognition of a hemi-methylated CpG site by SRA.
Figure 4: A successive DNA transfer model for maintenance DNA methylation by UHRF1 and Dnmt1.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structural factors for the reported structures have been deposited with the Protein Data Bank under accession codes 2ZKG (unliganded SRA), 2ZKD (SRA-5mCpG-1 DNA, monoclinic form), 2ZKE (SRA-5mCpG-1 DNA, tetragonal form), 2ZKF (SRA-5mCpG-2 DNA).


  1. Chen, R. Z. et al. DNA hypomethylation leads to elevated mutation rates. Nature 395, 89–93 (1998)

    Article  ADS  CAS  Google Scholar 

  2. Bird, A. & Wolffe, A. P. Methylation-induced repression—belts, braces, and chromatin. Cell 99, 451–454 (1999)

    Article  CAS  Google Scholar 

  3. Ballobio, A. & Willard, H. F. Mammalian X-chromosome inactivation and the XIST gene. Curr. Opin. Genet. Dev. 2, 439–447 (1992)

    Article  Google Scholar 

  4. Surani, M. A. Imprinting and the initiation of gene silencing in the germ line. Cell 93, 309–312 (1998)

    Article  CAS  Google Scholar 

  5. Xu, G. L. et al. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature 402, 187–191 (1999)

    Article  ADS  CAS  Google Scholar 

  6. Costello, J. F. et al. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nature Genet. 24, 132–138 (2000)

    Article  CAS  Google Scholar 

  7. Tajima, S. & Suetake, I. Regulation and function of DNA methylation in vertebrates. J. Biochem. 123, 993–999 (1998)

    Article  CAS  Google Scholar 

  8. Hermann, A., Gowher, H. & Jeltsch, A. Biochemistry and biology of mammalian DNA methyltransferases. Cell. Mol. Life Sci. 61, 2571–2587 (2004)

    Article  CAS  Google Scholar 

  9. Bostick, M. et al. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 317, 1760–1764 (2007)

    Article  ADS  CAS  Google Scholar 

  10. Sharif, J. et al. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 450, 908–912 (2007)

    Article  ADS  CAS  Google Scholar 

  11. Ooi, S. K. & Bestor, T. H. Cytosine methylation: remaining faithful. Curr. Biol. 18, R174–R176 (2008)

    Article  CAS  Google Scholar 

  12. Ohki, I. et al. Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA. Cell 105, 487–497 (2001)

    Article  CAS  Google Scholar 

  13. Ho, K. L. et al. MeCP2 binding to DNA depends upon hydration at methyl-CpG. Mol. Cell 29, 525–531 (2008)

    Article  CAS  Google Scholar 

  14. Klimasauskas, S., Kumar, S., Roberts, R. J. & Cheng, X. HhaI methyltransferase flips its target base out of the DNA helix. Cell 76, 357–369 (1994)

    Article  CAS  Google Scholar 

  15. Suck, D. DNA–protein interactions. Flip out and modify. Curr. Biol. 4, 252–255 (1994)

    Article  CAS  Google Scholar 

  16. Cheng, X. & Blumenthal, R. M. Finding a basis for flipping bases. Structure 4, 639–645 (1996)

    Article  CAS  Google Scholar 

  17. O’Gara, M., Roberts, R. J. & Cheng, X. A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase. J. Mol. Biol. 263, 597–606 (1996)

    Article  Google Scholar 

  18. Tubbs, J. L., Pegg, A. E. & Tainer, J. A. DNA binding, nucleotide flipping, and the helix–turn–helix motif in base repair by O6-alkylguanine-DNA alkyltransferase and its implications for cancer chemotherapy. DNA Repair (Amst.) 6, 1100–1115 (2007)

    Article  CAS  Google Scholar 

  19. Achour, M. et al. The interaction of the SRA domain of ICBP90 with a novel domain of DNMT1 is involved in the regulation of VEGF gene expression. Oncogene 27, 2187–2197 (2008)

    Article  CAS  Google Scholar 

  20. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

    Article  CAS  Google Scholar 

  21. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

  22. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991)

    Article  Google Scholar 

  23. Brunger, A. T. Version 1.2 of the Crystallography and NMR system. Nature Protocols 2, 2728–2733 (2007)

    Article  CAS  Google Scholar 

  24. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D. 53, 240–255 (1997)

    Article  CAS  Google Scholar 

  25. DeLano, W. L. The PyMOL Molecular Graphics System (DeLano Scientific, 2002)

    Google Scholar 

  26. Jones, S. & Thornton, J. M. Protein–protein interactions: a review of protein dimer structures. Prog. Biophys. Mol. Biol. 63, 31–59 (1995)

    Article  CAS  Google Scholar 

  27. Luscombe, N. M., Laskowski, R. A. & Thornton, J. M. NUCPLOT: a program to generate schematic diagrams of protein–nucleic acid interactions. Nucleic Acids Res. 25, 4940–4945 (1997)

    Article  CAS  Google Scholar 

Download references


We thank K. Morikawa for discussion, and N. Matsugaki, N. Igarashi, Y. Yamada, M. Suzuki and S. Wakatsuki for data collection at PF-BL5. This work was supported by grants to M.S. from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan and the Japan Science and Technology Agency, and by a Grant-in-Aid for Scientific Research to K.A. from the Japan Society for the Promotion of Science. The authors acknowledge support from the Global COE Program ‘Integrated Materials Science’ of MEXT of Japan.

Author information

Authors and Affiliations


Corresponding authors

Correspondence to Mariko Ariyoshi or Masahiro Shirakawa.

Supplementary information

Supplementary Information

The file contains Supplementary Results, Supplementary Figures 1-10 and Supplementary Tables 1-3. (PDF 1383 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Arita, K., Ariyoshi, M., Tochio, H. et al. Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism. Nature 455, 818–821 (2008).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing