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Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain

Nature volume 410, pages 120–124 (2001)Cite this article

Abstract

Heterochromatin protein 1 (HP1) is localized at heterochromatin sites where it mediates gene silencing1,2. The chromo domain of HP1 is necessary for both targeting and transcriptional repression3,4. In the fission yeast Schizosaccharomyces pombe, the correct localization of Swi6 (the HP1 equivalent) depends on Clr4, a homologue of the mammalian SUV39H1 histone methylase5,6. Both Clr4 and SUV39H1 methylate specifically lysine 9 of histone H3 (ref. 6). Here we show that HP1 can bind with high affinity to histone H3 methylated at lysine 9 but not at lysine 4. The chromo domain of HP1 is identified as its methyl-lysine-binding domain. A point mutation in the chromo domain, which destroys the gene silencing activity of HP1 in Drosophila3, abolishes methyl-lysine-binding activity. Genetic and biochemical analysis in S. pombe shows that the methylase activity of Clr4 is necessary for the correct localization of Swi6 at centromeric heterochromatin and for gene silencing. These results provide a stepwise model for the formation of a transcriptionally silent heterochromatin: SUV39H1 places a ‘methyl marker’ on histone H3, which is then recognized by HP1 through its chromo domain. This model may also explain the stable inheritance of the heterochromatic state.

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Figure 1: HP1 chromo domain binds methylated H3.
Figure 2: HP1 chromo domain specifically binds methylated Lys 9 of histone H3.
Figure 3: HP1 chromatin localization is dependent on binding to methylated K9 of H3.
Figure 4: Swi6 localization is dependent on the methylase activity of the Clr4 SET domain.
Figure 5

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Acknowledgements

We thank E. Laue and N. Murzina for his-HP1 clones, M33 and Mi2 clones, and for discussions on structure, and P. Chambon for GST-HP1 clones. We also thank D. Durocher for advice with SPR, T. Krude for guidance on nuclear preparations and M. Ruas for preparing some proteins. We are grateful to E. Andrews for help in the preparation of nucleosomes, and to E. Nimmo and P. Lord for the clr4-G341D allele. Peptides were synthesized by G. Bloomberg, Bristol University. This work was funded by a Cancer Research Campaign programme grant to T.K. and Medical Research Council core support to R.A. J.O.T. thanks the BBSRC for support.

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Author notes

  1. Andrew J. Bannister, Philip Zegerman and Jean O. Thomas: These authors contributed equally to this work

Authors and Affiliations

  1. Wellcome/CRC Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK

    Andrew J. Bannister, Philip Zegerman, Eric A. Miska & Tony Kouzarides

  2. MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK

    Janet F. Partridge & Robin C. Allshire

  3. Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK

    Jean O. Thomas

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  1. Andrew J. Bannister
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Correspondence to Tony Kouzarides.

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Bannister, A., Zegerman, P., Partridge, J. et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120–124 (2001). https://doi.org/10.1038/35065138

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