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Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component

Abstract

Post-translational modification of histone tails is thought to modulate higher-order chromatin structure1,2,3. Combinations of modifications including acetylation, phosphorylation and methylation have been proposed to provide marks recognized by specific proteins4. This is exemplified, in both mammalian cells and fission yeast, by transcriptionally silent constitutive pericentric heterochromatin. Such heterochromatin contains histones that are generally hypoacetylated5 and methylated by Suv39h methyltransferases at lysine 9 of histone H3 (H3-K9)6,7. Each of these modification states has been implicated in the maintenance of HP1 protein–binding at pericentric heterochromatin, in transcriptional silencing and in centromere function7,8,9,10,11,12. In particular, H3-K9 methylation is thought to provide a marking system for the establishment and maintenance of stably repressed regions and heterochromatin subdomains3,13. To address the question of how these two types of modifications, as well as other unidentified parameters, function to maintain pericentric heterochromatin, we used a combination of histone deacetylase inhibitors, RNAse treatments and an antibody raised against methylated branched H3-K9 peptides. Our results show that both H3-K9 acetylation and methylation can occur on independent sets of H3 molecules in pericentric heterochromatin. In addition, we identify an RNA- and histone modification–dependent structure that brings methylated H3-K9 tails together in a specific configuration required for the accumulation of HP1 proteins in these domains.

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Figure 1: Suv39h-dependent pericentric heterochromatin organization is differently recognized by two antibodies against methylated H3-K9.
Figure 2: The spatial organization of H3-K9 methylated tails in pericentric heterochromatin is disrupted by TSA treatment.
Figure 3: An RNA-dependent structural epitope recognized by branched α-methH3-K9 and α-HP1α antibodies at pericentromeric regions.
Figure 4: Distinct RNase sensitivity of pericentric heterochromatin and inactive X chromosome.

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References

  1. Rice, J.C. & Allis, C.D. Histone methylation versus histone acetylation: new insights into epigenetic regulation. Curr. Opin. Cell. Biol. 13, 263–273 (2001).

    Article  CAS  Google Scholar 

  2. Turner, B.M. Histone acetylation and an epigenetic code. Bioessays 22, 836–845 (2000).

    Article  CAS  Google Scholar 

  3. Jenuwein, T. & Allis, C.D. Translating the histone code. Science 293, 1074–1080 (2001).

    Article  CAS  Google Scholar 

  4. Strahl, B.D. & Allis, D.C. The language of covalent histone modifications. Nature 403, 41–45 (2000).

    Article  CAS  Google Scholar 

  5. Jeppesen, P., Mitchell, A., Turner, B. & Perry, P. Antibodies to defined histone epitopes reveal variations in chromatin conformation and underacetylation of centric heterochromatin in human metaphase chromosomes. Chromosoma 101, 322–332 (1992).

    Article  CAS  Google Scholar 

  6. Peters, A.H. et al. Loss of the suv39h histone methyltransferases impairs Mammalian heterochromatin and genome stability. Cell 107, 323–337 (2001).

    Article  CAS  Google Scholar 

  7. Nakayama, J., Rice, J.C., Strahl, B.D., Allis, C.D. & Grewal, S.I. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292, 110–113 (2001).

    Article  CAS  Google Scholar 

  8. Rea, S. et al. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406, 593–599 (2000).

    Article  CAS  Google Scholar 

  9. Bannister, A.J. et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120–124 (2001).

    Article  CAS  Google Scholar 

  10. Lachner, M., O'Carroll, D., Rea, S., Mechtler, K. & Jenuwein, T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410, 116–120 (2001).

    Article  CAS  Google Scholar 

  11. Taddei, A., Maison, C., Roche, D. & Almouzni, G. Reversible disruption of pericentric heterochromatin and centromere function by inhibiting deacetylases. Nature Cell Biol. 3, 114–120 (2001).

    Article  CAS  Google Scholar 

  12. Ekwall, K., Olsson, T., Turner, B.M., Cranston, G. & Allshire, R.C. Transient inhibition of histone deacetylation alters the structural and functional imprint at fission yeast centromeres. Cell 91, 1021–1032 (1997).

    Article  CAS  Google Scholar 

  13. Zhang, Y. & Reinberg, D. Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. Genes Dev. 15, 2343–2360 (2001).

    Article  CAS  Google Scholar 

  14. Cheung, P., Allis, C.D. & Sassone-Corsi, P. Signaling to chromatin through histone modifications. Cell 103, 263–271 (2000).

    Article  CAS  Google Scholar 

  15. Kipling, D., Wilson, H.E., Mitchell, A.R., Taylor, B.A. & Cooke, H.J. Mouse centromere mapping using oligonucleotide probes that detect variants of the minor satellite. Chromosoma 103, 46–55 (1994).

    Article  CAS  Google Scholar 

  16. Akhtar, A., Zink, D. & Becker, P.B. Chromodomains are protein-RNA interaction modules. Nature 407, 405–409 (2000).

    Article  CAS  Google Scholar 

  17. Jones, D.O., Cowell, I.G. & Singh, P.B. Mammalian chromodomain proteins: their role in genome organisation and expression. Bioessays 22, 124–137 (2000).

    Article  CAS  Google Scholar 

  18. Avner, P. & Heard, E. X-chromosome inactivation: counting, choice and initiation. Nature Rev. Genet. 2, 59–67 (2001).

    Article  CAS  Google Scholar 

  19. Lyon, M.F. X-chromosome inactivation. Curr. Biol. 9, R235–237 (1999).

    Article  CAS  Google Scholar 

  20. Peters, A.H.F.M. et al. Histone H3 lysine 9 methylation is an epigenetic imprint of facultative heterochromatin. Nature Genet. 30, 77–80 (2002).

    Article  CAS  Google Scholar 

  21. Boggs, B.A. et al. Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes. Nature Genet. 30, 73–76 (2002).

    Article  CAS  Google Scholar 

  22. Gasser, S.M. Positions of potential: nuclear organization and gene expression. Cell 104, 639–642 (2001).

    Article  CAS  Google Scholar 

  23. Jaeger, L. The New World of ribozymes. Curr. Opin. Struct. Biol. 7, 324–335 (1997).

    Article  CAS  Google Scholar 

  24. Nielsen, A.L. et al. Heterochromatin formation in mammalian cells: interaction between histones and HP1 proteins. Mol. Cell 7, 729–739 (2001).

    Article  CAS  Google Scholar 

  25. Jacobs, S.A. et al. Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J. 20, 5232–5241 (2001).

    Article  CAS  Google Scholar 

  26. Aagaard, L. et al. Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3- 9 encode centromere-associated proteins which complex with the heterochromatin component M31. EMBO J. 18, 1923–1938 (1999).

    Article  CAS  Google Scholar 

  27. Kornberg, R.D., LaPointe, J.W. & Lorch, Y. Preparation of nucleosomes and chromatin. Methods Enzymol. 170, 3–14 (1989).

    Article  CAS  Google Scholar 

  28. O'Neill, L.P. & Turner, B.M. Immunoprecipitation of chromatin. Methods Enzymol. 274, 189–197 (1996).

    Article  CAS  Google Scholar 

  29. Brown, K.E. et al. Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 91, 845–854 (1997).

    Article  CAS  Google Scholar 

  30. Martini, E., Roche, D.M.J., Marheineke, K., Verreault, A. & Almouzni, G. Recruitment of phosphorylated Chromatin Assembly Factor 1 to chromatin following UV irradiation of human cells. J. Cell Biol. 3, 563–575 (1998).

    Article  Google Scholar 

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Acknowledgements

We thank W. Earnshaw for the HP1α-GST clone, B. Dietrich, C. Green and E. Heard for critical reading, and A. Kohlmaier for help with the protein analysis of histone modifications in Suv39h double-negative PMEFs. Work in T.J.'s laboratory is supported by the Institute of Molecular Pathology through Boehringer Ingelheim and grants from the Austrian Research promotion fund, the Vienna Economy Promotion Fund and a European Union Intellectual Property network grant. Research in G.A.'s laboratory is supported by Ligue Nationale Contre le Cancer, Euratom and an EU Improving Human Potential network grant.

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Correspondence to Geneviève Almouzni.

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Maison, C., Bailly, D., Peters, A. et al. Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component. Nat Genet 30, 329–334 (2002). https://doi.org/10.1038/ng843

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