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Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2

Abstract

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.

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Figure 1: Structure of ING2 PHD finger in complex with a histone H3 peptide trimethylated at Lys 4.
Figure 2: ING2 PHD finger recognizes H3K4me3.
Figure 3: ING2 function requires its H3K4me3 binding activity.

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Acknowledgements

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.

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Correspondence to Tatiana G. Kutateladze.

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Competing interests

The coordinates have been deposited in the Protein Data Bank under accession number 2G6Q. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Supplementary information

Supplementary Figure 1

Alignment of PHD domain sequences: absolutely, moderately and weakly conserved residues are colored brown, green and yellow, respectively. (JPG 221 kb)

Supplementary Figure 2

Determination of the specificity of the ING2 PHD finger. (JPG 178 kb)

Supplementary Figure 3

Substitution of the active site residues of the ING2 PHD finger for Ala does not disrupt the structure. (JPG 176 kb)

Supplementary Notes

This file contains Supplementary Figure Legends and Supplementary Methods. (DOC 41 kb)

Supplementary Table

Data collection and refinement statistics. Table of X-ray statistics. (DOC 57 kb)

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Peña, P., Davrazou, F., Shi, X. et al. Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature 442, 100–103 (2006). https://doi.org/10.1038/nature04814

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