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Histone Modifications-Marks for Gene Expression?

  • Axel Imhof
Conference paper
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 544)

Abstract

During early embryonic development stable patterns of gene expression have to be established and maintained over several cell generations. In higher eukaryotes the activity of a particular gene has been shown to depend on a coordinated action of several classes of proteins and protein complexes ranging from chromatin remodelling machines to basal transcriptions factors and eventually the RNA polymerase itself. It is less clear how such a activated or repressed state is then maintained during subsequent cell divisions. Many transcription factors involved in gene activation or repression get transiently displaced from their binding sites during mitosis or disappear completely. Over the last few years, chromatin has been shown to play an important role in regulating gene expression and establishing stable patterns of gene activity in response to incoming signals (Cheung et al., 2000; Wolffe, 1998). The fundamental unit of chromatin, the nucleosome consists of an octamer made up by two molecules of each of the core histones H3, H2A, H2B and H4 around which 147bp of DNA are wrapped in 1.75 turns of a left handed superhelix. In the nucleosome the globular domains of the four core histones are folded in a compact hydrophobic core, whereas the N-termini extend into solution (Luger et al, 1997) (Figure 1).

Keywords

Histone Modification Polycomb Group Heterochromatin Formation Heterochromatin Domain Cell BioI 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. Ahmad, K. and Henikoff, S., 2001, Centromeres are specialized replication domains in heterochromatin. J. Cell Biol. 153: 101–110.PubMedCrossRefGoogle Scholar
  2. Bannister, A. J., Zegerman, P., Partridge, J. F., Miska, E. A., Thomas, J. O., Allshire, R. C. and Kouzarides, T., 2001, Selective recognition of methylated lysine 9 on histone H3 by the HP 1 chromo domain. Nature 410: 120–124.PubMedCrossRefGoogle Scholar
  3. Bauer, U. M., Daujat, S., Nielsen, S. J., Nightingale, K. and Kouzarides, T., 2002, Methylation at arginine 17 of histone H3 is linked to gene activation. EMBO Rep. 3: 39–44.PubMedCrossRefGoogle Scholar
  4. Beisel, C, Imhof, A., Greene, J., Kremmer, E. and Sauer, F., 2002, Histone methylation by the Drosophila epigenetic transcriptional regulator Ashl. Nature 419: 857–862.PubMedCrossRefGoogle Scholar
  5. Boggs, B. A., Cheung, P., Heard, E., Spector, D. L., Chinault, A. C. and Allis, C. D., 2002, Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes. Nat. Genet. 30: 73–76.PubMedCrossRefGoogle Scholar
  6. Braunstein, M., Sobel, R. E., Allis, C. D., Turner, B. M. and Broach, J. R., 1996, Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern. Mol. Cell Biol. 16: 4349–4356.PubMedGoogle Scholar
  7. Cavalli, G. and Paro, R., 1999, Epigenetic inheritance of active chromatin after removal of the main transactivator. Science 286: 955–958.PubMedCrossRefGoogle Scholar
  8. Chen, D., Ma, H., Hong, H., Koh, S. S., Huang, S. M., Schurter, B. T., Aswad, D. W. and Stallcup, M. R., 1999, Regulation of transcription by a protein methyltransferase. Science 284: 2174–2177.PubMedCrossRefGoogle Scholar
  9. Cheung, P., Allis, C. D. and Sassone-Corsi, P., 2000, Signaling to chromatin through histone modifications. Cell 103: 263–271.PubMedCrossRefGoogle Scholar
  10. Czermin, B., Melfi, R., McCabe, D., Seitz, V., Imhof, A. and Pirrotta, V., 2002, Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell, 111: 185–196.PubMedCrossRefGoogle Scholar
  11. Czermin, B., Schotta, G., Hulsmann, B. B., Brehm, A., Becker, P. B., Reuter, G. and Imhof, A., 2001, Physical and functional association of SU(VAR)3–9 and HDAC1 in Drosophila, EMBORep. 2:3–9.CrossRefGoogle Scholar
  12. Daujat, S., Bauer, U. M, Shah, V., Turner, B., Berger, S. and Kouzarides, T., 2002, Crosstalk between CARM1 Methylation and CBP Acetylation on Histone H3. Curr. Biol. 12: 2090–2097.PubMedCrossRefGoogle Scholar
  13. Espinos, E., Le Van Thai, A., Pomies, C. and Weber, M. J., 1999, Cooperation between phosphorylation and acetylation processes in transcriptional control. Mol. Cell Biol. 19: 3474–3484.PubMedGoogle Scholar
  14. Francis, N. J., Saurin, A. J., Shao, Z. and Kingston, R. E., 2001, Reconstitution of a functional core polycomb repressive complex. Mol. Cell 8: 545–56.PubMedCrossRefGoogle Scholar
  15. Hadorn, E., Gsell, R. and Schultz, J., 1970, Stability of a position-effect variegation in normal and transdetermined larval blastemas from Drosophila melanogaster. Proc. Natl. Acad. Sci. U. S. A. 65: 633–637.PubMedCrossRefGoogle Scholar
  16. Hall, I. M., Shankaranarayana, G. D., Noma, K., Ayoub, N., Cohen, A. and Grewal, S. I., 2002, Establishment and maintenance of a heterochromatin domain. Science 297: 2232–2237.PubMedCrossRefGoogle Scholar
  17. Heard, E., Rougeulle, C, Arnaud, D., Avner, P., Allis, C. D. and Spector, D. L., 2001, Methylation of histone H3 at Lys-9 is an early mark on the X chromosome during X inactivation. Cell 107: 727–738.PubMedCrossRefGoogle Scholar
  18. Hebbes, T. R., Clayton, A. L., Thome, A. W. and Crane-Robinson, C, 1994, Core histone hyperacetylation co-maps with generalized DNase I sensitivity in the chicken beta-globin chromosomal domain. Embo J. 13: 1823–1830.PubMedGoogle Scholar
  19. Hecht, A., Laroche, T., Strahl-Bolsinger, S., Gasser, S. M. and Grunstein, M., 1995, Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast. Cell 80: 583–592.PubMedCrossRefGoogle Scholar
  20. Henikoff, S., 2000, Heterochromatin function in complex genomes. Biochim. Biophys. Acta, 1470: 01–8.Google Scholar
  21. Imhof, A., 2003, Histone modifications: an assembly line for active chromatin? Curr. Biol. 13: R22–24.PubMedCrossRefGoogle Scholar
  22. Imhof, A. and Becker, P. B., 2001, Modifications of the histone N-terminal domains. Evidence for an “epigenetic code”? Mol. Biotechnol. 17: 1–13.PubMedCrossRefGoogle Scholar
  23. Imhof, A. and Wolffe, A. P., 1998, Transcription: gene control by targeted histone acetylation. Curr. Biol. 8: R422–424.PubMedCrossRefGoogle Scholar
  24. Jenuwein, T. and Allis, C. D., 2001, Translating the histone code. Science, 293: 1074–1080.PubMedCrossRefGoogle Scholar
  25. Jeppesen, P. and Turner, B. M., 1993, The inactive X chromosome in female mammals is distinguished by a lack of histone H4 acetylation, a cytogenetic marker for gene expression. Cell 74:281–289.PubMedCrossRefGoogle Scholar
  26. Kelly, T. J., Qin, S., Gottschling, D. E. and Parthun, M. R., 2000, Type B histone acetyltransferase Hatlp participates in telomeric silencing. Mol. Cell Biol. 19, 7051–7058.CrossRefGoogle Scholar
  27. Lachner, M., O’Carroll, D., Rea, S., Mechtler, K. and Jenuwein, T., 2001, Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410: 116–120.PubMedCrossRefGoogle Scholar
  28. Litt, M. D., Simpson, M., Gaszner, M., Allis, C. D. and Felsenfeld, G., 2001, Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus. Science 293: 2453–2455.PubMedCrossRefGoogle Scholar
  29. Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F. and Richmond, T. J., 1997, Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389: 251–260.PubMedCrossRefGoogle Scholar
  30. Mahadevan, L. C, Willis, A. C. and Barratt, M. J., 1991, Rapid histone H3 phosphorylation in response to growth factors, phorbol esters, okadaic acid, and protein synthesis inhibitors. Cell 65: 775–783.PubMedCrossRefGoogle Scholar
  31. Mottus, R., Sobel, R. E. and Grigliatti, T. A., 2000, Mutational analysis of a histone deacetylase in Drosophila melanogaster: missense mutations suppress gene silencing associated with position effect variegation. Genetics 154: 657–668.PubMedGoogle Scholar
  32. Muller, H. J., 1930, Types of visible variations induced by X-rays in Drosophila melanogaster, J. Genet. 22: 299–334.CrossRefGoogle Scholar
  33. Noma, K., Allis, C. D. and Grewal, S. I., 2001, Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293: 1150–1155.PubMedCrossRefGoogle Scholar
  34. O’Connell, S., Wang, L., Robert, S., Jones, C. A., Saint, R. and Jones, R. S., 2001, Polycomblike PHD fingers mediate conserved interaction with enhancer of zeste protein. J. Biol Chem. 276: 43065–43073.PubMedCrossRefGoogle Scholar
  35. Parekh, B. S. and Maniatis, T., 1999, Virus infection leads to localized hyperacetylation of histones H3 and H4 at the IFN-beta promoter. Mol. Cell 3: 125–129.PubMedCrossRefGoogle Scholar
  36. Pirrotta, V., 1999, Polycomb silencing and the maintenance of stable chromatin states, Results Probl Cell Differ. 25: 205–228.PubMedGoogle Scholar
  37. Poux, S., Mem, R. and Pirrotta, V., 2001, Establishment of Polycomb silencing requires a transient interaction between PC and ESC. Genes Dev. 15: 2509–2514.PubMedCrossRefGoogle Scholar
  38. Rea, S., Eisenhaber, F., O’Carroll, D., Strahl, B. D., Sun, Z. W., Schmid, M., Opravil, S., Mechtler, K., Ponting, C. P., Allis, C. D. and Jenuwein, T., 2000, Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406: 593–599.PubMedCrossRefGoogle Scholar
  39. Richards, E. J. and Elgin, S. C, 2002, Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell 108: 489–500.PubMedCrossRefGoogle Scholar
  40. Saurin, A. J., Shao, Z., Erdjument-Bromage, H., Tempst, P. and Kingston, R. E., 2001, A Drosophila Polycomb group complex includes Zeste and dTAFII proteins. Nature 412: 655–660.PubMedCrossRefGoogle Scholar
  41. Schotta, G., Ebert, A., Dorn, R. and Reuter, G., 2003, Position-effect variegation and the genetic dissection of chromatin regulation in Drosophila. Semin. Cell Dev. Biol 14: 67–75.PubMedCrossRefGoogle Scholar
  42. Schotta, G., Ebert, A., Krauss, V., Fischer, A., Hoffmann, J., Rea, S., Jenuwein, T., Dorn, R. and Reuter, G., 2002, Central role of Drosophila SU(VAR)3–9 in histone 3–9 methylation and heterochromatic gene silencing. Embo J. 21,3–9.PubMedCrossRefGoogle Scholar
  43. Sewalt, R. G., van der Vlag, J., Gunster, M. J., Hamer, K. M., den Blaauwen, J. L., Satijn, D. P., Hendrix, T., van Driel, R. and Otte, A. P., 1998, Characterization of interactions between the mammalian polycomb-group proteins Enxl/EZH2 and EED suggests the existence of different mammalian polycomb-group protein complexes. Mol Cell Biol. 18: 3586–3595.PubMedGoogle Scholar
  44. Simon, J., Bornemann, D., Lunde, K. and Schwartz, C, 1995, The extra sex combs product contains WD40 repeats and its time of action implies a role distinct from other Polycomb group products. Mech. Ztev.53: 197–208.Google Scholar
  45. Struhl, G. and Brower, D., 1982, Early role of the esc+ gene product in the determination of segments in Drosophila. Cell 31, 285–292.PubMedCrossRefGoogle Scholar
  46. Taddei, A., Roche, D., Sibarita, J. B., Turner, B. M. and Almouzni, G., 1999, Duplication and maintenance of heterochromatin domains. J. Cell Biol 147: 1153–1166.PubMedCrossRefGoogle Scholar
  47. Talbert, P. B. and Henikoff, S., 2000, A reexamination of spreading of position-effect variegation in the white-roughest region of Drosophila melanogaster. Genetics 154: 259–272.PubMedGoogle Scholar
  48. Tartof, K. D., Hobbs, C. and Jones, M, 1984, A structural basis for variegating position effects. Cell 37: 869–878.PubMedCrossRefGoogle Scholar
  49. Tie, F., Furuyama, T., Prasad-Sinha, J., Jane, E. and Harte, P. J., 2001, The Drosophila Polycomb Group proteins ESC and E(Z) are present in a complex containing the histone-binding protein p55 and the histone deacetylase RPD3. Development 128: 275–286.PubMedGoogle Scholar
  50. Tschiersch, B., Hofmann, A., Krauss, V., Dorn, R., Korge, G. and Reuter, G., 1994, The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3–9 combines domains of antagonistic regulators of homeotic gene complexes. Embo J. 13: 3–9.PubMedGoogle Scholar
  51. Turner, B. M, 2000, Histone acetylation and an epigenetic code. Bioessays 22: 836–845.PubMedCrossRefGoogle Scholar
  52. Turner, B. M., Birley, A. J. and Lavender, J., 1992, Histone H4 isoforms acetylated at specific lysine residues define individual chromosomes and chromatin domains in Drosophila polytene nuclei. Cell 69: 375–384.PubMedCrossRefGoogle Scholar
  53. Utley, R. T., Ikeda, K., Grant, P. A., Cote, J., Steger, D. J., Eberharter, A., John, S. and Workman, J. L., 1998, Transcriptional activators direct histone acetyltransferase complexes to nucleosomes. Nature, 394: 498–502.PubMedCrossRefGoogle Scholar
  54. van Lohuizen, M., 1998, Functional analysis of mouse Polycomb group genes. Cell Mol Life Sci. 54: 71–79.PubMedCrossRefGoogle Scholar
  55. Vaute, O., Nicolas, E., Vandel, L. and Trouche, D., 2002, Functional and physical interaction between the histone methyl transferase Suv39Hl and histone deacetylases. Nucleic Acids Res. 30: 475–481.PubMedCrossRefGoogle Scholar
  56. Wade, P. A., Jones, P. L., Vermaak, D., Veenstra, G. J., Imhof, A., Sera, T., Tse, C, Ge, H., Shi, Y. B., Hansen, J. C. and Wolffe, A. P., 1998, Histone deacetylase directs the dominant silencing of transcription in chromatin: association with MeCP2 and the Mi-2 chromodomain SWI/SNF ATPase. Cold Spring Harb. Symp. Quant. Biol. 63: 435–445.PubMedCrossRefGoogle Scholar
  57. Wei, Y., Yu, L., Bowen, J., Gorovsky, M. A. and Allis, C. D., 1999, Phosphorylation of histone H3 is required for proper chromosome condensation and segregation. Cell 97: 99–109.PubMedCrossRefGoogle Scholar
  58. Wolffe AP. 1998. Chromatin Structure and Function, 3rd ed. San Diego, CA: Academic Press. 447 p.Google Scholar
  59. Wong, J., Patterton, D., Imhof, A., Guschin, D., Shi, Y. B. and Wolffe, A. P., 1998, Distinct requirements for chromatin assembly in transcriptional repression by thyroid hormone receptor and histone deacetylase. Embo J . 17: 520–534.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2003

Authors and Affiliations

  • Axel Imhof
    • 1
  1. 1.Adolf-Butenandt Institut University of MunichMuenchenGERMANY

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