Advertisement

The European Physical Journal E

, Volume 19, Issue 3, pp 379–384 | Cite as

Chromatin physics: Replacing multiple, representation-centered descriptions at discrete scales by a continuous, function-dependent self-scaled model

Focus Point

Abstract.

This commentary on the inspiring works and ideas by Langowski, Mangeol et al., Lee et al., Bundschuh and Gerland, Schiessel, Vaillant et al., Lesne and Victor, Claudet and Bednar, Fuks, Allemand et al., and Blossey, all appearing in this issue (Eur. Phys. J. E 19 (2006)), expresses our felt need of novel approaches to chromatin modeling.

PACS.

87.15.Aa Theory and modeling; computer simulation 87.16.-b Subcellular structure and processes 87.16.Sr Chromosomes, histones 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    J.D. Watson, F.H. Crick, Nature 171, 737 (1953).ADSGoogle Scholar
  2. 2.
    H.E. Avery, C.M. MacLeod, M. McCarty, J. Exp. Med. 79, 137 (1944).CrossRefGoogle Scholar
  3. 3.
    U. Bockelmann, Curr. Opin. Struct. Biol. 14, 368 (2004).CrossRefGoogle Scholar
  4. 4.
    P. Mangeol, Probing DNA and RNA single molecules with a double optical tweezer, this issue, p. 311.Google Scholar
  5. 5.
    C.H. Lee, Comparison of the measured phase diagrams in the force-temperature plane for the unzipping of two different natural DNA sequences, this issue, p. 339.Google Scholar
  6. 6.
    C. Anselmi, Biophys. Chem. 95, 23 (2002).CrossRefGoogle Scholar
  7. 7.
    T.E. Cloutier, J. Widom, Proc. Natl. Acad. Sci. U.S.A. 102, 3645 (2005).CrossRefADSGoogle Scholar
  8. 8.
    J. Yan, J.F. Marko, Phys. Rev. Lett. 93, 108108 (2004).CrossRefADSGoogle Scholar
  9. 9.
    M.T. Rivero, Exp. Cell Res. 295, 161 (2004).CrossRefGoogle Scholar
  10. 10.
    A.E. Vinogradov, Nucleic Acids Res. 31, 1838 (2003).CrossRefGoogle Scholar
  11. 11.
    R. Bundschuh, U. Gerland, Dynamics of intramolecular recognition: Base-pairing in DNA/RNA near and far from equilibrium, this issue, p. 319.Google Scholar
  12. 12.
    S.E. Halford, J.F. Marko, Nucleic Acids Res. 32, 3040 (2004).CrossRefGoogle Scholar
  13. 13.
    R.V. Polozov, J. Biomol. Struct. Dyn. 16, 1135 (1999).Google Scholar
  14. 14.
    A. Bird, Genes Dev. 16, 6 (2002).CrossRefGoogle Scholar
  15. 15.
    K.D. Robertson, Nat. Rev. Genet. 6, 597 (2005).CrossRefGoogle Scholar
  16. 16.
    T.M. Geiman, K.D. Robertson, J. Cell. Biochem. 87, 117 (2002).CrossRefGoogle Scholar
  17. 17.
    R.D. Kornberg, Science 184, 868 (1974).ADSGoogle Scholar
  18. 18.
    M. Noll, Nature 251, 249 (1974).CrossRefADSGoogle Scholar
  19. 19.
    R.D. Kornberg, Y. Lorch, Cell 98, 285 (1999).CrossRefGoogle Scholar
  20. 20.
    R.T. Kamakaka, S. Biggins, Genes Dev. 19, 295 (2005).CrossRefGoogle Scholar
  21. 21.
    C.L. Peterson, M.A. Laniel, Curr. Biol. 14, R546 (2004).Google Scholar
  22. 22.
    A. Sivolob, C. Lavelle, A. Prunell, J. Mol. Biol. 326, 49 (2003).CrossRefGoogle Scholar
  23. 23.
    H. Schiessel, The nucleosome: A transparent, slippery, sticky and yet stable DNA-protein complex, this issue, p. 251.Google Scholar
  24. 24.
    A. Sivolob, A. Prunell, Philos. Trans. R. Soc. London, Ser. A 362, 1519 (2004).MathSciNetMATHGoogle Scholar
  25. 25.
    F. De Lucia, J. Mol. Biol. 285, 1101 (1999).CrossRefGoogle Scholar
  26. 26.
    A. Bancaud, Structural dynamics of single chromatin fibres revealed by torsional manipulation, submitted.Google Scholar
  27. 27.
    C. Lavelle, A. Sivolob, A. Prunell, in preparation.Google Scholar
  28. 28.
    C.P. Prior, Cell 34, 1033 (1983).CrossRefGoogle Scholar
  29. 29.
    J. Mozziconacci, J.M. Victor, J. Struct. Biol. 143, 72 (2003).CrossRefGoogle Scholar
  30. 30.
    M. Alilat, J. Mol. Biol. 291, 815 (1999).CrossRefGoogle Scholar
  31. 31.
    A. Hamiche, Proc. Natl. Acad. Sci. U.S.A. 93, 7588 (1996).CrossRefADSGoogle Scholar
  32. 32.
    P.B. Becker, EMBO J. 21, 4749 (2002).CrossRefGoogle Scholar
  33. 33.
    A. Flaus, T. Owen-Hughes, Curr. Opin. Genet. Dev. 14, 165 (2004).CrossRefGoogle Scholar
  34. 34.
    C.J. Brandl, K. Struhl, Mol. Cell. Biol. 10, 4256 (1990).Google Scholar
  35. 35.
    M. Kanduri, Mol. Cell. Biol. 22, 3339 (2002).CrossRefGoogle Scholar
  36. 36.
    N. Gilbert, J. Allan, Proc. Natl. Acad. Sci. U.S.A. 98, 11949 (2001).CrossRefADSGoogle Scholar
  37. 37.
    C. Vaillant, Formation and positioning of nucleosomes: Effect of sequence-dependent long-range correlated structural disorder, this issue, p. 263.Google Scholar
  38. 38.
    Y.Y. Hsu, Y.H. Wang, J. Biol. Chem. 277, 17315 (2002).CrossRefGoogle Scholar
  39. 39.
    D.T. Kirkpatrick, Mol. Cell. Biol. 19, 7661 (1999).Google Scholar
  40. 40.
    C. Anselmi, Biophys. J. 79, 601 (2000).CrossRefGoogle Scholar
  41. 41.
    V.G. Levitsky, Nucleic Acids Res. 32 (Web Server issue), W346-9 (2004).Google Scholar
  42. 42.
    A. Lesne, J.-M. Victor, Chromatin fiber functional organization: Some plausible models, this issue, p. 279.Google Scholar
  43. 43.
    J. Zlatanova, S.H. Leuba, J. Mol. Biol. 331, 1 (2003).CrossRefGoogle Scholar
  44. 44.
    C. Claudet, J. Bednar, Pulling the chromatin, this issue, p. 331.Google Scholar
  45. 45.
    T.A. Blank, P.B. Becker, J. Mol. Biol. 252, 305 (1995).CrossRefGoogle Scholar
  46. 46.
    F. Fuks, The view from the biochemist, this issue, p. 367.Google Scholar
  47. 47.
    A. Benecke, Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs, this issue, p. 353.Google Scholar
  48. 48.
    Y. Huyen, Nature 432, 406 (2004).CrossRefADSGoogle Scholar
  49. 49.
    S. Henikoff, Y. Dalal, Curr. Opin. Genet. Dev. 15, 177 (2005).CrossRefGoogle Scholar
  50. 50.
    E.R. Foster, J.A. Downs, FEBS J. 272, 3231 (2005).CrossRefGoogle Scholar
  51. 51.
    A.S. Belmont, Curr. Opin. Cell. Biol. 11, 307 (1999).CrossRefGoogle Scholar
  52. 52.
    A.S. Belmont, K. Bruce, J. Cell. Biol. 127, 287 (1994).CrossRefGoogle Scholar
  53. 53.
    K. Byrd, V.G. Corces, J. Cell. Biol. 162, 565 (2003).CrossRefGoogle Scholar
  54. 54.
    D. Sproul, N. Gilbert, W.A. Bickmore, Nat. Rev. Genet. 6, 775 (2005).CrossRefGoogle Scholar
  55. 55.
    D. Carter, Nat. Genet. 32, 623 (2002).CrossRefGoogle Scholar
  56. 56.
    P.R. Cook, J. Cell. Sci. 116, 4483 (2003).CrossRefADSGoogle Scholar
  57. 57.
    J.R. Swedlow, T. Hirano, Mol. Cell 11, 557 (2003).CrossRefGoogle Scholar
  58. 58.
    B.D. Lavoie, E. Hogan, D. Koshland, J. Cell. Biol. 156, 805 (2002).CrossRefGoogle Scholar
  59. 59.
    S. Almagro, J. Biol. Chem. 279, 5118 (2004).CrossRefGoogle Scholar
  60. 60.
    J.F. Marko, M.G. Poirier, Biochem. Cell. Biol. 81, 209 (2003).CrossRefGoogle Scholar
  61. 61.
    J. Mozziconacci, FEBS Lett. 580, 368 (2006).CrossRefGoogle Scholar
  62. 62.
    T. Cremer, C. Cremer, Nat. Rev. Genet. 2, 292 (2001).CrossRefGoogle Scholar
  63. 63.
    T. Cremer, Biol. Cell 96, 555 (2004).CrossRefGoogle Scholar
  64. 64.
    T. Misteli, Bioessays 27, 477 (2005).CrossRefGoogle Scholar
  65. 65.
    S. Kozubek, Chromosoma 108, 426 (1999).CrossRefGoogle Scholar
  66. 66.
    T. Misteli, Cell 119, 153 (2004).CrossRefGoogle Scholar
  67. 67.
    L. Parada, T. Misteli, Trends Cell. Biol. 12, 425 (2002).CrossRefGoogle Scholar
  68. 68.
    L.A. Parada, P.G. McQueen, T. Misteli, Genome Biol. 5, R44 (2004). Google Scholar
  69. 69.
    D. Gerlich, Cell 112, 751 (2003).CrossRefGoogle Scholar
  70. 70.
    E.M. Manders, Chromosome Res. 11, 537 (2003).CrossRefGoogle Scholar
  71. 71.
    J. Langowski, Polymer chain models of DNA and chromatin, this issue, p. 241.Google Scholar
  72. 72.
    G. Li, Nat. Struct. Mol. Biol. 12, 46 (2005).CrossRefGoogle Scholar
  73. 73.
    S. Henikoff, T. Furuyama, K. Ahmad, Trends Genet. 20, 320 (2004).CrossRefGoogle Scholar
  74. 74.
    R. Blossey, Regulating chromatin: On code and dynamic models, this issue, p. 371.Google Scholar
  75. 75.
    J.-F. Allemand, Loops in DNA: An overview of experimental and theoretical approaches, this issue, p. 293.Google Scholar

Copyright information

© EDP Sciences, Società Italiana di Fisica and Springer-Verlag 2006

Authors and Affiliations

  1. 1.Radiobiology and Oncology GroupCommissariat à l'Energie AtomiqueFontenay-aux-RosesFrance
  2. 2.System Epigenomics GroupInstitut des Hautes Etudes Scientifiques - Institut de Recherches Interdisciplinaires - CNRS/INSERMBures-sur-YvetteFrance

Personalised recommendations