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Abstract

Dynamic regulation of diverse nuclear processes is intimately linked to covalent modifications of chromatin1,2. Much attention has focused on methylation at lysine 4 of histone H3 (H3K4), owing to its association with euchromatic genomic regions3,4. H3K4 can be mono-, di- or tri-methylated. Trimethylated H3K4 (H3K4me3) is preferentially detected at active genes, and is proposed to promote gene expression through recognition by transcription-activating effector molecules5. Here we identify a novel class of methylated H3K4 effector domains—the PHD domains of the ING (for inhibitor of growth) family of tumour suppressor proteins. The ING PHD domains are specific and highly robust binding modules for H3K4me3 and H3K4me2. ING2, a native subunit of a repressive mSin3a–HDAC1 histone deacetylase complex6, binds with high affinity to the trimethylated species. In response to DNA damage, recognition of H3K4me3 by the ING2 PHD domain stabilizes the mSin3a–HDAC1 complex at the promoters of proliferation genes. This pathway constitutes a new mechanism by which H3K4me3 functions in active gene repression. Furthermore, ING2 modulates cellular responses to genotoxic insults, and these functions are critically dependent on ING2 interaction with H3K4me3. Together, our findings establish a pivotal role for trimethylation of H3K4 in gene repression and, potentially, tumour suppressor mechanisms.

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Acknowledgements

We thank Y. Zhang for the SET7 expression vector, C. Harris for ING3, ING4 and ING5 complementary DNAs, J. Wysocka and W. Herr for a WDR5 antibody, J. Wysocka and C. D. Allis for communicating unpublished results, J. Yuan for ING2 antibodies and A. Sanchez for peptide synthesis. This work was supported by NIH grants to O.G., Y.S. and B.R.C. O.G. is a recipient of a Burroughs Wellcome Career Development Award in Biomedical Sciences.

Author information

Affiliations

  1. Department of Biological Sciences, Stanford University, and

    • Xiaobing Shi
    • , Kay L. Walter
    • , Mark Ewalt
    • , Tiffany Hung
    • , Dylan Carney
    •  & Or Gozani
  2. Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA

    • Tao Hong
    • , Eriko Michishita
    •  & Katrin F. Chua
  3. Department of Pharmacology, University of Colorado Health Sciences Center, Aurora, Colorado 80045, USA

    • Pedro Peña
    • , Foteini Davrazou
    •  & Tatiana G. Kutateladze
  4. Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Fei Lan
    •  & Yang Shi
  5. Huntsman Cancer Institute and Department of Oncological Sciences, University of Utah, Salt Lake City, Utah 84112, USA

    • Mohan R. Kaadige
    • , Anjanabha Saha
    • , Bradley R. Cairns
    •  & Donald E. Ayer
  6. Laval University Cancer Research Center, Quebec City, Quebec G1R 2J6, Canada

    • Nicolas Lacoste
    • , Christelle Cayrou
    •  & Jacques Côté
  7. Geriatric Research, Education and Clinical Center, VA Palo Alto Health Care System, Palo Alto, California 94304, USA

    • Katrin F. Chua

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Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

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Correspondence to Or Gozani.

Supplementary information

Word documents

  1. 1.

    Supplementary Notes

    This file contains the Supplementary Methods, Supplementary Figure Legends and additional references. (1). Nature14097-S1

Image files

  1. 1.

    Supplementary Figure 1

    ING2 PHD domain specifically binds in vitro to trimethylated Lysine 4 of histone H3.

  2. 2.

    Supplementary Figure 2

    The ING2 PHD domain D230A mutation specifically abrogates methylated H3K4 binding but not PtdIns(5)P-binding.

  3. 3.

    Supplementary Figure 3

    ING2(PHD) association with H3 is correlated with K4 methylation level in vitro.

  4. 4.

    Supplementary Figure 4

    Methyl-lysine recognition is a property of at least a subset of PHD domains.

  5. 5.

    Supplementary Figure 5

    Silver-stained gels of affinity-purified wild-type and mutant ING2 macromolecular complexes.

  6. 6.

    Supplementary Figure 6

    ING2 occupancy across the cyclin D1 gene correlates with the presence of methylated-H3K4.

  7. 7.

    Supplementary Figure 7

    DNA damage-dependent increased ING2 occupancy at the c-Myc promoter requires H3- triMeK4-binding activity.

  8. 8.

    Supplementary Figure 8

    Model of acute transcriptional repression mediated by ING2 recognition of trimethylated H3K4.

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DOI

https://doi.org/10.1038/nature04835

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