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Heterochromatin protein 1 forms distinct complexes to direct histone deacetylation and DNA methylation

Nature Structural & Molecular Biology volume 19, pages 471–477 (2012)Cite this article

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Abstract

DNA methylation, methylation of histone H3 at Lys9 (H3K9me3) and hypoacetylated histones are common molecular features of heterochromatin. Important details of their functions and inter-relationships remain unclear, however. In Neurospora crassa, H3K9me3 directs DNA methylation through a complex containing heterochromatin protein 1 (HP1) and the DNA methyltransferase DIM-2. We identified a distinct HP1 complex, HP1, CDP-2, HDA-1 and CHAP (HCHC), and found that it is responsible for silencing independently of DNA methylation. HCHC defects cause hyperacetylation of centromeric histones, greater accessibility of DIM-2 and hypermethylation of centromeric DNA. Loss of HCHC also causes mislocalization of the DIM-5 H3K9 methyltransferase at a subset of interstitial methylated regions, leading to selective DNA hypomethylation. We demonstrate that HP1 forms distinct DNA methylation and histone deacetylation complexes that work in parallel to assemble silent chromatin in N. crassa.

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Figure 1: Aberrant DNA methylation in the cdp-2 mutant.
Figure 2: The CDP-2 chromodomain preferentially binds to H3K9 methylation and CDP-2 stability depends on HP1.
Figure 3: Mutation of cdp-2 causes lower H3K9me3 and HP1 localization at hypomethylated regions but no difference at hypermethylated regions compared with wild type.
Figure 4: CDP-2 is required for DIM-5 recruitment to regions with moderate RIP.
Figure 5: Identification of HCHC.
Figure 6: HCHC is required for normal histone H3 and H4 acetylation.
Figure 7: DIM-2 accessibility at centromere is enhanced in cdp-2 mutant.
Figure 8: HCHC is required for centromere silencing independent of DNA methylation.

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Acknowledgements

We thank L.L. David and members of his proteomics facility at Oregon Health Sciences University for identifying DIM-2-associated proteins and T. Khalafallah for technical support in preliminary work. E.U.S. thanks S. Gasser and D. Schübeler (F. Miescher Institute) and G. Almouzni (Institut Curie) for hosting him during a sabbatical. This work was funded by grant GM025690 to E.U.S. from the US National Institutes of Health. We acknowledge the Neurospora Genome Project and the Fungal Genetic Stock Center for providing materials.

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Author notes

  1. Shinji Honda & Zachary A Lewis

    Present address: Present addresses: Life Science Unit, University of Fukui, Fukui, Japan (S.H.); Department of Microbiology, University of Georgia, Athens, Georgia, USA (Z.A.L.).,

Authors and Affiliations

  1. Department of Biology and Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA

    Shinji Honda, Zachary A Lewis & Eric U Selker

  2. Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland

    Kenji Shimada & Ragna Sack

  3. Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany

    Wolfgang Fischle

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Contributions

S.H. and E.U.S. designed the research. Z.A.L. and E.U.S. carried out the MeDIP-chip experiments; E.U.S. and K.S. carried out CDP-2 purification; R.S. carried out mass spectrometry to identify CDP-2-associated proteins; W.F. carried out anisotropic binding assays to determine the CDP-2 chromodomain binding activity and S.H. carried out the other experiments. S.H., Z.A.L. and E.U.S. analyzed the data; S.H. and E.U.S. wrote the paper and Z.A.L., K.S. W.F. and R.S. edited the paper.

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Correspondence to Eric U Selker.

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Supplementary Figures 1–8, Supplementary Tables 1 and 2 and Supplementary Methods (PDF 1274 kb)

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Honda, S., Lewis, Z., Shimada, K. et al. Heterochromatin protein 1 forms distinct complexes to direct histone deacetylation and DNA methylation. Nat Struct Mol Biol 19, 471–477 (2012). https://doi.org/10.1038/nsmb.2274

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