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The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier–Gorlin syndrome

Nature volume 484, pages 115–119 (2012)Cite this article

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Abstract

The recognition of distinctly modified histones by specialized ‘effector’ proteins constitutes a key mechanism for transducing molecular events at chromatin to biological outcomes1. Effector proteins influence DNA-templated processes, including transcription, DNA recombination and DNA repair; however, no effector functions have yet been identified within the mammalian machinery that regulate DNA replication. Here we show that ORC1—a component of ORC (origin of replication complex), which mediates pre-DNA replication licensing2—contains a bromo adjacent homology (BAH) domain that specifically recognizes histone H4 dimethylated at lysine 20 (H4K20me2). Recognition of H4K20me2 is a property common to BAH domains present within diverse metazoan ORC1 proteins. Structural studies reveal that the specificity of the BAH domain for H4K20me2 is mediated by a dynamic aromatic dimethyl-lysine-binding cage and multiple intermolecular contacts involving the bound peptide. H4K20me2 is enriched at replication origins, and abrogating ORC1 recognition of H4K20me2 in cells impairs ORC1 occupancy at replication origins, ORC chromatin loading and cell-cycle progression. Mutation of the ORC1 BAH domain has been implicated in the aetiology of Meier–Gorlin syndrome (MGS)3,4, a form of primordial dwarfism5, and ORC1 depletion in zebrafish results in an MGS-like phenotype4. We find that wild-type human ORC1, but not ORC1–H4K20me2-binding mutants, rescues the growth retardation of orc1 morphants. Moreover, zebrafish depleted of H4K20me2 have diminished body size, mirroring the phenotype of orc1 morphants. Together, our results identify the BAH domain as a novel methyl-lysine-binding module, thereby establishing the first direct link between histone methylation and the metazoan DNA replication machinery, and defining a pivotal aetiological role for the canonical H4K20me2 mark, via ORC1, in primordial dwarfism.

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Figure 1: The ORC1 BAH domain is a novel H4K20me2-binding module.
Figure 2: The molecular basis of H4K20me2 recognition by ORC1BAH.
Figure 3: ORC1–H4K20me2 interaction regulates ORC chromatin association and cell-cycle progression.
Figure 4: Disruption of the ORC1 BAH –H4K20me2 interaction leads to dwarfism in zebrafish.

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Acknowledgements

We thank R. Tennen for critical reading of the manuscript. This work was supported in part by grants to O.G. (R01 GM079641), D.J.P. (Abby Rockefeller Mauze, STARR and Maloris Foundations) and J.K.C. (DP1 OD003792), and a predoctoral fellowship to A.J.K. (Genentech Foundation). O.G. is a recipient of an Ellison Senior Scholar in Aging Award.

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Author notes

  1. Jikui Song

    Present address: Present address: Department of Biochemistry, University of California, Riverside, California 92521, USA.,

  2. Alex J. Kuo, Jikui Song and Peggie Cheung: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biology, Stanford University, Stanford, 94305, California, USA

    Alex J. Kuo, Peggie Cheung & Or Gozani

  2. Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, 10065, New York, USA

    Jikui Song, Satoko Ishibe-Murakami & Dinshaw J. Patel

  3. Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford, 94305, California, USA

    Sayumi Yamazoe & James K. Chen

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Contributions

A.J.K. and P.C. performed the molecular biology, cellular and zebrafish studies; J.S. performed structural and binding affinity studies; S.Y. and J.K.C. advised on zebrafish experiments; S.I.-M. assisted in protein production and crystallization. A.J.K., P.C., J.S., D.J.P. and O.G. designed studies, analysed data and wrote the paper. All authors discussed and commented on the manuscript.

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Correspondence to Dinshaw J. Patel or Or Gozani.

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Kuo, A., Song, J., Cheung, P. et al. The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier–Gorlin syndrome. Nature 484, 115–119 (2012). https://doi.org/10.1038/nature10956

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