Covalent modifications of histone tails have a key role in regulating chromatin structure and controlling transcriptional activity. In eukaryotes, histone H3 trimethylated at lysine 4 (H3K4me3) is associated with active chromatin and gene expression1,2,3,4. We recently found that plant homeodomain (PHD) finger of tumour suppressor ING2 (inhibitor of growth 2) binds H3K4me3 and represents a new family of modules that target this epigenetic mark5. The molecular mechanism of H3K4me3 recognition, however, remains unknown. Here we report a 2.0 Å resolution structure of the mouse ING2 PHD finger in complex with a histone H3 peptide trimethylated at lysine 4. The H3K4me3 tail is bound in an extended conformation in a deep and extensive binding site consisting of elements that are conserved among the ING family of proteins. The trimethylammonium group of Lys 4 is recognized by the aromatic side chains of Y215 and W238 residues, whereas the intermolecular hydrogen-bonding and complementary surface interactions, involving Ala 1, Arg 2, Thr 3 and Thr 6 of the peptide, account for the PHD finger's high specificity and affinity. Substitution of the binding site residues disrupts H3K4me3 interaction in vitro and impairs the ability of ING2 to induce apoptosis in vivo. Strong binding of other ING and YNG PHD fingers suggests that the recognition of H3K4me3 histone code is a general feature of the ING/YNG proteins. Elucidation of the mechanisms underlying this novel function of PHD fingers provides a basis for deciphering the role of the ING family of tumour suppressors in chromatin regulation and signalling.
Access optionsAccess options
Subscribe to Journal
Get full journal access for 1 year
only $3.90 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Santos-Rosa, H. et al. Active genes are tri-methylated at K4 of histone H3. Nature 419, 407–411 (2002)
Schneider, R. et al. Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nature Cell Biol. 6, 73–77 (2004)
Briggs, S. D. et al. Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes Dev. 15, 3286–3295 (2001)
Sims, R. J. III, Nishioka, K. & Reinberg, D. Histone lysine methylation: a signature for chromatin function. Trends Genet. 19, 629–639 (2003)
Shi, X. et al. ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature doi:10.1038/nature04835 (2006).
Strahl, B. D. & Allis, C. D. The language of covalent histone modifications. Nature 403, 41–45 (2000)
Dhalluin, C. et al. Structure and ligand of a histone acetyltransferase bromodomain. Nature 399, 491–496 (1999)
Jacobson, R. H., Ladurner, A. G., King, D. S. & Tjian, R. Structure and function of a human TAFII250 double bromodomain module. Science 288, 1422–1425 (2000)
Bannister, A. J. et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120–124 (2001)
Lachner, M., O'Carroll, D., Rea, S., Mechtler, K. & Jenuwein, T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410, 116–120 (2001)
Nielsen, P. R. et al. Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9. Nature 416, 103–107 (2002)
Jacobs, S. A. & Khorasanizadeh, S. Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science 295, 2080–2083 (2002)
Flanagan, J. F. et al. Double chromodomains cooperate to recognize the methylated histone H3 tail. Nature 438, 1181–1185 (2005)
Ragvin, A. et al. Nucleosome binding by the bromodomain and PHD finger of the transcriptional cofactor p300. J. Mol. Biol. 337, 773–788 (2004)
Eberharter, A., Vetter, I., Ferreira, R. & Becker, P. B. ACF1 improves the effectiveness of nucleosome mobilization by ISWI through PHD-histone contacts. EMBO J. 23, 4029–4039 (2004)
Pascual, J., Martinez-Yamout, M., Dyson, H. J. & Wright, P. E. Structure of the PHD zinc finger from human Williams-Beuren syndrome transcription factor. J. Mol. Biol. 304, 723–729 (2000)
Fischle, W. et al. Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev. 17, 1870–1881 (2003)
Min, J., Zhang, Y. & Xu, R. M. Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev. 17, 1823–1828 (2003)
Nagashima, M. et al. DNA damage-inducible gene p33ING2 negatively regulates cell proliferation through acetylation of p53. Proc. Natl Acad. Sci. USA 98, 9671–9676 (2001)
Doyon, Y. et al. ING tumor suppressor proteins are critical regulators of chromatin acetylation required for genome expression and perpetuation. Mol. Cell 21, 51–64 (2006)
Campos, E. I., Chin, M. Y., Kuo, W. H. & Li, G. Biological functions of the ING family tumor suppressors. Cell. Mol. Life Sci. 61, 2597–2613 (2004)
Loewith, R., Meijer, M., Lees-Miller, S. P., Riabowol, K. & Young, D. Three yeast proteins related to the human candidate tumor suppressor p33(ING1) are associated with histone acetyltransferase activities. Mol. Cell. Biol. 20, 3807–3816 (2000)
Kuzmichev, A., Zhang, Y., Erdjument-Bromage, H., Tempst, P. & Reinberg, D. Role of the Sin3-histone deacetylase complex in growth regulation by the candidate tumor suppressor p33(ING1). Mol. Cell. Biol. 22, 835–848 (2002)
Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)
Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991)
Brünger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)
Grzesiek, S., Stahl, S. J., Wingfield, P. T. & Bax, A. The CD4 determinant for downregulation by HIV-1 Nef directly binds to Nef. Mapping of the Nef binding surface by NMR. Biochemistry 35, 10256–10261 (1996)
We thank D. Bentley and J. Tyler for discussions; M. Grunstein for providing GST fusion histone tails; B. Tripet and the Biophysics Core Facility for synthesis of the histone peptides; the University of Colorado Health Sciences Center's X-ray Core Facility and NMR Core Facility, supported by the University of Colorado Cancer Center; and A. Heroux and the mail-in data collection service at the National Synchrotron Light Source (NSLS) for synchrotron data collection. Financial support for NSLS comes principally from the Offices of Biological and Environmental Research and of Basic Energy Sciences of the US Department of Energy, and from the National Center for Research Resources of the National Institutes of Health (NIH). This research was supported by grants from the NIH (V.V.V., O.G. and T.G.K.), Burroughs Welcome (O.G.), American Heart Association (T.G.K.) and University of Colorado Cancer Center (T.G.K.). T.G.K. is a NARSAD Young Investigator and an American Cancer Society Research Scholar.
Alignment of PHD domain sequences: absolutely, moderately and weakly conserved residues are colored brown, green and yellow, respectively. (JPG 221 kb)
Determination of the specificity of the ING2 PHD finger. (JPG 178 kb)
Substitution of the active site residues of the ING2 PHD finger for Ala does not disrupt the structure. (JPG 176 kb)
This file contains Supplementary Figure Legends and Supplementary Methods. (DOC 41 kb)
Data collection and refinement statistics. Table of X-ray statistics. (DOC 57 kb)
About this article
Epigenetics & Chromatin (2019)
Tumor-promoting properties of miR-8084 in breast cancer through enhancing proliferation, suppressing apoptosis and inducing epithelial–mesenchymal transition
Journal of Translational Medicine (2018)
ING5 activity in self-renewal of glioblastoma stem cells via calcium and follicle stimulating hormone pathways
Family-Wide Characterization of Histone Binding Abilities of PHD Domains of AL Proteins in Arabidopsis thaliana
The Protein Journal (2018)
Nature Reviews Molecular Cell Biology (2017)