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

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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Figure 1: XIST RNA FISH combined with immunofluorescence staining on human female IMR 90 cells.
Figure 2: Immunofluorescence patterns of human metaphase chromosomes stained with the Lys9-methyl H3 antibody.
Figure 3: Immunofluorescence patterns of human metaphase chromosomes.
Figure 4: ChIP analysis of somatic cell hybrid cell lines. Chromatin from CHO somatic hybrid cells containing the inactive (Xinactive) or active (Xactive) human X chromosome was immunoprecipitated using the antibodies indicated.

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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.

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Correspondence to C. David Allis.

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Boggs, B., Cheung, P., Heard, E. et al. Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes. Nat Genet 30, 73–76 (2002). https://doi.org/10.1038/ng787

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