Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism (original) (raw)

Nature volume 455, pages 818–821 (2008)Cite this article

Abstract

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.

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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).

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Acknowledgements

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.

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Authors and Affiliations

  1. Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
    Kyohei Arita, Mariko Ariyoshi, Hidehito Tochio & Masahiro Shirakawa
  2. Japan Science and Technology Agency, CREST, 4-1-18, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan ,
    Hidehito Tochio & Masahiro Shirakawa
  3. Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan ,
    Yusuke Nakamura
  4. RIKEN, Yokohama Institute, Suehirocho, Tsurumi, Yokohama 230-0045, Japan ,
    Masahiro Shirakawa

Authors

  1. Kyohei Arita
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  2. Mariko Ariyoshi
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  3. Hidehito Tochio
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  4. Yusuke Nakamura
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  5. Masahiro Shirakawa
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Corresponding authors

Correspondence toMariko Ariyoshi or Masahiro Shirakawa.

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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). https://doi.org/10.1038/nature07249

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Editorial Summary

Keeping DNA methylation on track

DNA methylation is a key epigenetic process and the faithful maintenance of DNA methylation patterns is essential to the wellbeing of mammalian cells. This means that cells need a mechanism to identify the partially methylated version of CpG once a new DNA strand has been replicated or repaired, so that it can be further methylated by the DNA methyltransferase, DNMT1. As part of this process the protein UHRF1 (or Np95/ICBP90) facilitates the loading of DNMT1 onto the hemimethylated CpG sequences during DNA replication. Three papers in this issue describe crystal structures of the SRA domain of UHRF1 bound to DNA containing a hemi-methylated CpG site. The structures show that methyl-cytosine is flipped out of the DNA helix and inserted into a binding pocket on the SRA domain.