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The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules

Abstract

Histone modifications have important roles in transcriptional control, mitosis and heterochromatin formation. G9a and G9a-like protein (GLP) are euchromatin-associated methyltransferases that repress transcription by mono- and dimethylating histone H3 at Lys9 (H3K9). Here we demonstrate that the ankyrin repeat domains of G9a and GLP bind with strong preference to N-terminal H3 peptides containing mono- or dimethyl K9. X-ray crystallography revealed the basis for recognition of the methylated lysine by a partial hydrophobic cage with three tryptophans and one acidic residue. Substitution of key residues in the cage eliminated the H3 tail interaction. Hence, G9a and GLP contain a new type of methyllysine binding module (the ankyrin repeat domains) and are the first examples of protein (histone) methyltransferases harboring in a single polypeptide the activities that generate and read the same epigenetic mark.

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Figure 1: G9a and G9a-like protein (GLP) bind to mono- and dimethylated histone H3.
Figure 2: Structural basis for ankyrin repeat recognition of dimethylated histone H3 lysine 9 (H3K9me2).
Figure 3: Analysis of G9a ankyrin mutants that lack H3K9me1 and H3K9me2 peptide binding.

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Acknowledgements

We thank A. Ruiz and D. Gerke for technical assistance. The Emory University School of Medicine supported the use of SER-CAT beamlines. This work was supported by grants DK55274 to M.R.S. and GM068680 to X.C. from the US National Institutes of Health.

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R.E.C. and J.R.H. performed X-ray crystallography; R.E.C. and X.Z. performed fluorescence anisotropy. Other protein-protein interaction assays and histone methyltransferase assays were performed by J.P.N. and D.Y.L. The project was directed by M.R.S. and X.C. All authors contributed to the preparation of the manuscript.

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Correspondence to Michael R Stallcup or Xiaodong Cheng.

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Collins, R., Northrop, J., Horton, J. et al. The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules. Nat Struct Mol Biol 15, 245–250 (2008). https://doi.org/10.1038/nsmb.1384

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