ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression

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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Figure 1: The ING2 PHD domain specifically binds to H3K4me3 in vitro.
Figure 2: Methylated H3K4 recognition by the ING2 PHD domain enhances ING2-associated HDAC1 histone deacetylase activity in vitro.
Figure 3: The ING2 interaction with trimethylated H3K4 occurs in vivo and requires an intact PHD domain.
Figure 4: Recognition of H3K4me3 by ING2 PHD domain in vivo is critical for ING2 function.

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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and ING5 complementary DNAs, J. Wysocka and W. Herr for a WDR5 antibody, J. Wysocka and C. D. Allis for communicating unpublished results, J. Yuan for ING2 antibodies and A. Sanchez for peptide synthesis.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.

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Correspondence to Or Gozani.

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Supplementary information

Supplementary Notes

This file contains the Supplementary Methods, Supplementary Figure Legends and additional references. (1). Nature14097-S1 (DOC 197 kb)

Supplementary Figure 1

ING2 PHD domain specifically binds in vitro to trimethylated Lysine 4 of histone H3. (JPG 147 kb)

Supplementary Figure 2

The ING2 PHD domain D230A mutation specifically abrogates methylated H3K4 binding but not PtdIns(5)P-binding. (JPG 92 kb)

Supplementary Figure 3

ING2(PHD) association with H3 is correlated with K4 methylation level in vitro. (JPG 53 kb)

Supplementary Figure 4

Methyl-lysine recognition is a property of at least a subset of PHD domains. (JPG 75 kb)

Supplementary Figure 5

Silver-stained gels of affinity-purified wild-type and mutant ING2 macromolecular complexes. (JPG 53 kb)

Supplementary Figure 6

ING2 occupancy across the cyclin D1 gene correlates with the presence of methylated-H3K4. (JPG 99 kb)

Supplementary Figure 7

DNA damage-dependent increased ING2 occupancy at the c-Myc promoter requires H3- triMeK4-binding activity. (JPG 37 kb)

Supplementary Figure 8

Model of acute transcriptional repression mediated by ING2 recognition of trimethylated H3K4. (JPG 144 kb)

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Shi, X., Hong, T., Walter, K. et al. ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 442, 96–99 (2006). https://doi.org/10.1038/nature04835

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