Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1 (original) (raw)

Nature volume 455, pages 822–825 (2008)Cite this article

Abstract

Epigenetic inheritance in mammals is characterized by high-fidelity replication of CpG methylation patterns during development1,2. UHRF1 (also known as ICBP90 in humans and Np95 in mouse)3 is an E3 ligase important for the maintenance of global and local DNA methylation in vivo4,5. The preferential affinity of UHRF1 for hemi-methylated DNA over symmetrically methylated DNA by means of its SET and RING-associated (SRA) domain6 and its association with the maintenance DNA methyltransferase 1 (DNMT1) suggests a role in replication of the epigenetic code4,5,7. Here we report the 1.7 Å crystal structure of the apo SRA domain of human UHRF1 and a 2.2 Å structure of its complex with hemi-methylated DNA, revealing a previously unknown reading mechanism for methylated CpG sites (mCpG). The SRA–DNA complex has several notable structural features including a binding pocket that accommodates the 5-methylcytosine that is flipped out of the duplex DNA. Two specialized loops reach through the resulting gap in the DNA from both the major and the minor grooves to read the other three bases of the CpG duplex. The major groove loop confers both specificity for the CpG dinucleotide and discrimination against methylation of deoxycytidine of the complementary strand. The structure, along with mutagenesis data, suggests how UHRF1 acts as a key factor for DNMT1 maintenance methylation through recognition of a fundamental unit of epigenetic inheritance, mCpG.

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Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported crystal structures have been deposited with the Protein Data Bank under accession codes 3BI7 (SRA apo protein) and 3CLZ (SRA–DNA complex).

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Acknowledgements

We thank F. Chedin, A. Edwards and R. Klose for discussions, and A. Dong for collecting data at the synchrotron. Diffraction data were measured at the Advanced Photon Source (Argonne, Illinois), which was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract no. DE-AC02-06CH11357. The Structural Genomics Consortium is a registered charity (number 1097737) that receives funds from the Canadian Institutes for Health Research, the Canadian Foundation for Innovation, Genome Canada through the Ontario Genomics Institute, GlaxoSmithKline, Karolinska Institutet, the Knut and Alice Wallenberg Foundation, the Ontario Innovation Trust, the Ontario Ministry for Research and Innovation, Merck & Co., Inc., the Novartis Research Foundation, the Swedish Agency for Innovation Systems, the Swedish Foundation for Strategic Research and the Wellcome Trust. This research was also supported by the Canadian Cancer Society (S.D. and C.H.A.).

Author Contributions S.D.-P., G.V.A., J.R.W., C.B. and C.H.A. developed the experimental design. S.D.-P. designed and S.D. and Y.L. prepared plasmids for bacterial expression of recombinant proteins. G.V.A. and S.X. performed purification, characterization and crystallization of proteins and EMSA. J.R.W. designed the oligonucleotides and conducted the structural analysis. S.D.-P., C.H.A., J.R.W. and G.V.A. interpreted results and wrote the manuscript.

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Author notes

  1. George V. Avvakumov and John R. Walker: These authors contributed equally to this work.

Authors and Affiliations

  1. Structural Genomics Consortium, University of Toronto, 100 College Street, Toronto, Ontario M5G 1L5, Canada ,
    George V. Avvakumov, John R. Walker, Sheng Xue, Yanjun Li, Cheryl H. Arrowsmith & Sirano Dhe-Paganon
  2. Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada,
    Shili Duan & Cheryl H. Arrowsmith
  3. Département de Pharmacologie et Pharmacochimie des Interactions cellulaires et moléculaires, CNRS UMR 7175, IGL, Université Louis Pasteur Strasbourg I, Faculté de Pharmacie, 74 route du Rhin, B.P. 60024, 67401 Illkirch, France,
    Christian Bronner
  4. Department of Physiology, University of Toronto, 100 College Street, Toronto, Ontario M5G 1L5, Canada,
    Sirano Dhe-Paganon

Authors

  1. George V. Avvakumov
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  2. John R. Walker
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  3. Sheng Xue
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  4. Yanjun Li
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  5. Shili Duan
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  6. Christian Bronner
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  7. Cheryl H. Arrowsmith
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  8. Sirano Dhe-Paganon
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Corresponding author

Correspondence toSirano Dhe-Paganon.

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Avvakumov, G., Walker, J., Xue, S. et al. Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1.Nature 455, 822–825 (2008). https://doi.org/10.1038/nature07273

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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.