Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

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

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.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

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.

References

  1. Taverna, S. D., Li, H., Ruthenburg, A. J., Allis, C. D. & Patel, D. J. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nature Struct. Mol. Biol. 14, 1025–1040 (2007)

    Article  CAS  Google Scholar 

  2. Duncker, B. P., Chesnokov, I. N. & McConkey, B. J. The origin recognition complex protein family. Genome Biol. 10, 214 (2009)

    Article  Google Scholar 

  3. Bicknell, L. S. et al. Mutations in the pre-replication complex cause Meier-Gorlin syndrome. Nature Genet. 43, 356–359 (2011)

    Article  CAS  Google Scholar 

  4. Bicknell, L. S. et al. Mutations in ORC1, encoding the largest subunit of the origin recognition complex, cause microcephalic primordial dwarfism resembling Meier-Gorlin syndrome. Nature Genet. 43, 350–355 (2011)

    Article  CAS  Google Scholar 

  5. Klingseisen, A. & Jackson, A. P. Mechanisms and pathways of growth failure in primordial dwarfism. Genes Dev. 25, 2011–2024 (2011)

    Article  CAS  Google Scholar 

  6. Kouzarides, T. Chromatin modifications and their function. Cell 128, 693–705 (2007)

    Article  CAS  Google Scholar 

  7. Callebaut, I., Courvalin, J. C. & Mornon, J. P. The BAH (bromo-adjacent homology) domain: a link between DNA methylation, replication and transcriptional regulation. FEBS Lett. 446, 189–193 (1999)

    Article  CAS  Google Scholar 

  8. Onishi, M., Liou, G. G., Buchberger, J. R., Walz, T. & Moazed, D. Role of the conserved Sir3-BAH domain in nucleosome binding and silent chromatin assembly. Mol. Cell 28, 1015–1028 (2007)

    Article  CAS  Google Scholar 

  9. Sampath, V. et al. Mutational analysis of the Sir3 BAH domain reveals multiple points of interaction with nucleosomes. Mol. Cell. Biol. 29, 2532–2545 (2009)

    Article  CAS  Google Scholar 

  10. Armache, K. J., Garlick, J. D., Canzio, D., Narlikar, G. J. & Kingston, R. E. Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 Å resolution. Science 334, 977–982 (2011)

    Article  ADS  CAS  Google Scholar 

  11. Bua, D. J. et al. Epigenome microarray platform for proteome-wide dissection of chromatin-signaling networks. PLoS ONE 4, e6789 (2009)

    Article  ADS  Google Scholar 

  12. Bell, S. P., Mitchell, J., Leber, J., Kobayashi, R. & Stillman, B. The multidomain structure of Orc1p reveals similarity to regulators of DNA replication and transcriptional silencing. Cell 83, 563–568 (1995)

    Article  CAS  Google Scholar 

  13. Dorn, E. S. & Cook, J. G. Nucleosomes in the neighborhood: new roles for chromatin modifications in replication origin control. Epigenetics 6, 552–559 (2011)

    Article  CAS  Google Scholar 

  14. Bell, S. P. & Dutta, A. DNA replication in eukaryotic cells. Annu. Rev. Biochem. 71, 333–374 (2002)

    Article  CAS  Google Scholar 

  15. Zhang, Z., Hayashi, M. K., Merkel, O., Stillman, B. & Xu, R. M. Structure and function of the BAH-containing domain of Orc1p in epigenetic silencing. EMBO J. 21, 4600–4611 (2002)

    Article  CAS  Google Scholar 

  16. Botuyan, M. V. et al. Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair. Cell 127, 1361–1373 (2006)

    Article  CAS  Google Scholar 

  17. Li, H. et al. Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger. Mol. Cell 28, 677–691 (2007)

    Article  CAS  Google Scholar 

  18. Schotta, G. et al. A chromatin-wide transition to H4K20 monomethylation impairs genome integrity and programmed DNA rearrangements in the mouse. Genes Dev. 22, 2048–2061 (2008)

    Article  CAS  Google Scholar 

  19. Noguchi, K., Vassilev, A., Ghosh, S., Yates, J. L. & DePamphilis, M. L. The BAH domain facilitates the ability of human Orc1 protein to activate replication origins in vivo. EMBO J. 25, 5372–5382 (2006)

    Article  CAS  Google Scholar 

  20. Tardat, M. et al. The histone H4 Lys 20 methyltransferase PR-Set7 regulates replication origins in mammalian cells. Nature Cell Biol. 12, 1086–1093 (2010)

    Article  CAS  Google Scholar 

  21. Tardat, M., Murr, R., Herceg, Z., Sardet, C. & Julien, E. PR-Set7-dependent lysine methylation ensures genome replication and stability through S phase. J. Cell Biol. 179, 1413–1426 (2007)

    Article  CAS  Google Scholar 

  22. Miotto, B. & Struhl, K. HBO1 histone acetylase is a coactivator of the replication licensing factor Cdt1. Genes Dev. 22, 2633–2638 (2008)

    Article  CAS  Google Scholar 

  23. Kitsberg, D., Selig, S., Keshet, I. & Cedar, H. Replication structure of the human β-globin gene domain. Nature 366, 588–590 (1993)

    Article  ADS  CAS  Google Scholar 

  24. Guernsey, D. L. et al. Mutations in origin recognition complex gene ORC4 cause Meier-Gorlin syndrome. Nature Genet. 43, 360–364 (2011)

    Article  CAS  Google Scholar 

  25. Sun, X. J. et al. Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes. PLoS ONE 3, e1499 (2008)

    Article  ADS  Google Scholar 

  26. Costas, C. et al. Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks. Nature Struct. Mol. Biol. 18, 395–400 (2011)

    Article  CAS  Google Scholar 

  27. Miotto, B. & Struhl, K. HBO1 histone acetylase activity is essential for DNA replication licensing and inhibited by Geminin. Mol. Cell 37, 57–66 (2010)

    Article  CAS  Google Scholar 

  28. Jacob, Y. et al. Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases. Nature 466, 987–991 (2010)

    Article  ADS  CAS  Google Scholar 

  29. Brustel, J., Tardat, M., Kirsh, O., Grimaud, C. & Julien, E. Coupling mitosis to DNA replication: the emerging role of the histone H4-lysine 20 methyltransferase PR-Set7. Trends Cell Biol. 21, 452–460 (2011)

    Article  CAS  Google Scholar 

  30. Oda, H. et al. Monomethylation of histone H4-lysine 20 is involved in chromosome structure and stability and is essential for mouse development. Mol. Cell. Biol. 29, 2278–2295 (2009)

    Article  CAS  Google Scholar 

  31. Shi, X. et al. ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 442, 96–99 (2006)

    Article  ADS  CAS  Google Scholar 

  32. Matthews, A. G. et al. RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination. Nature 450, 1106–1110 (2007)

    Article  ADS  CAS  Google Scholar 

  33. Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948–1954 (2002)

    Article  Google Scholar 

  34. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

    Article  Google Scholar 

  35. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007)

    Article  CAS  Google Scholar 

  36. Mendez, J. & Stillman, B. Chromatin association of human origin recognition complex, Cdc6, and minichromosome maintenance proteins during the cell cycle: assembly of prereplication complexes in late mitosis. Mol. Cell. Biol. 20, 8602–8612 (2000)

    Article  CAS  Google Scholar 

  37. Kuo, A. J. et al. NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming. Mol. Cell 44, 609–620 (2011)

    Article  CAS  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

Authors

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.

Corresponding authors

Correspondence to Dinshaw J. Patel or Or Gozani.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-11 and Supplementary Table 1. (PDF 1855 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature10956

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing