Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation

Abstract

A fundamental challenge in mammalian biology has been the elucidation of mechanisms linking DNA methylation and histone post-translational modifications. Human UHRF1 (ubiquitin-like PHD and RING finger domain–containing 1) has multiple domains that bind chromatin, and it is implicated genetically in the maintenance of DNA methylation. However, molecular mechanisms underlying DNA methylation regulation by UHRF1 are poorly defined. Here we show that UHRF1 association with methylated histone H3 Lys9 (H3K9) is required for DNA methylation maintenance. We further show that UHRF1 association with H3K9 methylation is insensitive to adjacent H3 S10 phosphorylation—a known mitotic 'phospho-methyl switch'. Notably, we demonstrate that UHRF1 mitotic chromatin association is necessary for DNA methylation maintenance through regulation of the stability of DNA methyltransferase-1. Collectively, our results define a previously unknown link between H3K9 methylation and the faithful epigenetic inheritance of DNA methylation, establishing a notable mitotic role for UHRF1 in this process.

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Figure 1: The UHRF1 TTD binds H3K9me regardless of neighboring H3S10ph.
Figure 2: A structural basis for UHRF1 TTD insensitivity to H3S10ph.
Figure 3: Chromatin targeting of UHRF1 in mitosis is required for the maintenance of DNA methylation.
Figure 4: Chromatin targeting of UHRF1 in mitosis is required for the stability of DNMT1.
Figure 5: Proposed interaction between UHRF1, DNMT1 and H3K9 methylated histones in replicating and mitotic chromatin.

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Acknowledgements

We thank members of the Strahl laboratory for helpful discussions and H. Fried (University of North Carolina (UNC) Chapel Hill) for critical reading of the manuscript. We also thank the North Carolina Biotechnology Center (NCBC) and the UNC School of Medicine for support in the establishment of the High Throughput Peptide Synthesis and Array Core Facility at UNC Chapel Hill. This work was supported by research grants from the US National Institutes of Health (GM085394) to B.D.S. and (T32CA09156) to S.B.R., the NCBC (2010-IDG-I003) to B.D.S., the Cancer Prevention and Research Institute of Texas (RP110471) to M.T.B., the Natural Sciences and Engineering Research Council of Canada to C.H.A. and the Ontario Ministry of Health and Long-Term Care to C.H.A. and N.N. The Structural Genomics Consortium is a registered charity (no. 1097737) that receives funds from the Canadian Institutes of Health Research, Eli Lilly Canada, Genome Canada, GlaxoSmithKline, the Ontario Ministry of Economic Development and Innovation, the Novartis Research Foundation, Pfizer, Abbott, Takeda and the Wellcome Trust. C.H.A. holds a Canada Research Chair in Structural Genomics.

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S.B.R. and B.D.S. designed experiments. S.B.R. performed and analyzed peptide array, biophysical, molecular biology and cellular studies. K.K. performed peptide synthesis and contributed to data analysis. N.N., W.T., S.X. and C.H.A. designed, performed and analyzed structural studies. A.I.B. and J.Y.M. contributed to cloning and protein production. D.B.-L. produced lentivirus. S.M.F. and M.T.B. contributed key technical assistance and reagents for array studies. S.B.R., N.N., C.H.A. and B.D.S. wrote the manuscript.

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Correspondence to Brian D Strahl.

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Rothbart, S., Krajewski, K., Nady, N. et al. Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation. Nat Struct Mol Biol 19, 1155–1160 (2012). https://doi.org/10.1038/nsmb.2391

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