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Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes

Nature Genetics volume 30, pages 7376 (2002) | Download Citation

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Abstract

Studies of histone methylation have shown that H3 can be methylated at lysine 4 (Lys4) or lysine 9 (Lys9)1,2. Whereas H3–Lys4 methylation has been correlated with active gene expression3, H3–Lys9 methylation has been linked to gene silencing and assembly of heterochromatin in mouse and Schizosaccharomyces pombe4,5,6,7. The chromodomain of mouse HP1 (and Swi6 in S. pombe) binds H3 methylated at Lys9, and methylation at this site is thought to mark and promote heterochromatin assembly. We have used a well-studied model of mammalian epigenetic silencing, the human inactive X chromosome, to show that enrichment for H3 methylated at Lys9 is also a distinguishing mark of facultative heterochromatin. In contrast, H3 methylated at Lys4 is depleted in the inactive X chromosome, except in three 'hot spots' of enrichment along its length. Chromatin immunoprecipitation analyses further show that Lys9 methylation is associated with promoters of inactive genes, whereas Lys4 methylation is associated with active genes on the X chromosome. These data demonstrate that differential methylation at two distinct sites of the H3 amino terminus correlates with contrasting gene activities and may be part of a 'histone code' involved in establishing and maintaining facultative heterochromatin.

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Acknowledgements

We thank M.A. Jelinek and R. Rice (Upstate Biotechnology) for technical assistance in generating the methyl H3-specific antibodies, and A. Baldini for helpful discussions. This work was funded by National Institutes of Health grants to C.D.A., A.C.C. and D.L.S. E.H. was supported by NATO and the Centre National de la Recherche Scientifique.

Author information

Author notes

    • Edith Heard

    Present address: CNRS UMR 218, Curie Institute, 26, rue d'Ulm, 75248 Paris Cedex 05, France.

    • Barbara A. Boggs
    •  & Peter Cheung

    These authors contributed equally to this work.

Affiliations

  1. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.

    • Barbara A. Boggs
    •  & A. Craig Chinault
  2. Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA.

    • Peter Cheung
    •  & C. David Allis
  3. Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724, USA.

    • Edith Heard
    •  & David L. Spector

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Correspondence to C. David Allis.

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DOI

https://doi.org/10.1038/ng787

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