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Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1

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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Figure 1: Structure of the SRA domain of UHRF1 and its DNA-bound form.
Figure 2: The methylcytosine-binding pocket.
Figure 3: SRA domain specificity determinants.
Figure 4: Role of the NKR finger in the DNA binding.

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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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Correspondence to Sirano 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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