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

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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.

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References

  1. J.D. Watson, F.H. Crick, Nature 171, 737 (1953).

    ADS  Google Scholar 

  2. H.E. Avery, C.M. MacLeod, M. McCarty, J. Exp. Med. 79, 137 (1944).

    Article  Google Scholar 

  3. U. Bockelmann, Curr. Opin. Struct. Biol. 14, 368 (2004).

    Article  Google Scholar 

  4. P. Mangeol, Probing DNA and RNA single molecules with a double optical tweezer, this issue, p. 311.

  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.

  6. C. Anselmi, Biophys. Chem. 95, 23 (2002).

    Article  Google Scholar 

  7. T.E. Cloutier, J. Widom, Proc. Natl. Acad. Sci. U.S.A. 102, 3645 (2005).

    Article  ADS  Google Scholar 

  8. J. Yan, J.F. Marko, Phys. Rev. Lett. 93, 108108 (2004).

    Article  ADS  Google Scholar 

  9. M.T. Rivero, Exp. Cell Res. 295, 161 (2004).

    Article  Google Scholar 

  10. A.E. Vinogradov, Nucleic Acids Res. 31, 1838 (2003).

    Article  Google Scholar 

  11. R. Bundschuh, U. Gerland, Dynamics of intramolecular recognition: Base-pairing in DNA/RNA near and far from equilibrium, this issue, p. 319.

  12. S.E. Halford, J.F. Marko, Nucleic Acids Res. 32, 3040 (2004).

    Article  Google Scholar 

  13. R.V. Polozov, J. Biomol. Struct. Dyn. 16, 1135 (1999).

    Google Scholar 

  14. A. Bird, Genes Dev. 16, 6 (2002).

    Article  Google Scholar 

  15. K.D. Robertson, Nat. Rev. Genet. 6, 597 (2005).

    Article  Google Scholar 

  16. T.M. Geiman, K.D. Robertson, J. Cell. Biochem. 87, 117 (2002).

    Article  Google Scholar 

  17. R.D. Kornberg, Science 184, 868 (1974).

    ADS  Google Scholar 

  18. M. Noll, Nature 251, 249 (1974).

    Article  ADS  Google Scholar 

  19. R.D. Kornberg, Y. Lorch, Cell 98, 285 (1999).

    Article  Google Scholar 

  20. R.T. Kamakaka, S. Biggins, Genes Dev. 19, 295 (2005).

    Article  Google Scholar 

  21. C.L. Peterson, M.A. Laniel, Curr. Biol. 14, R546 (2004).

  22. A. Sivolob, C. Lavelle, A. Prunell, J. Mol. Biol. 326, 49 (2003).

    Article  Google Scholar 

  23. H. Schiessel, The nucleosome: A transparent, slippery, sticky and yet stable DNA-protein complex, this issue, p. 251.

  24. A. Sivolob, A. Prunell, Philos. Trans. R. Soc. London, Ser. A 362, 1519 (2004).

    MathSciNet  MATH  Google Scholar 

  25. F. De Lucia, J. Mol. Biol. 285, 1101 (1999).

    Article  Google Scholar 

  26. A. Bancaud, Structural dynamics of single chromatin fibres revealed by torsional manipulation, submitted.

  27. C. Lavelle, A. Sivolob, A. Prunell, in preparation.

  28. C.P. Prior, Cell 34, 1033 (1983).

    Article  Google Scholar 

  29. J. Mozziconacci, J.M. Victor, J. Struct. Biol. 143, 72 (2003).

    Article  Google Scholar 

  30. M. Alilat, J. Mol. Biol. 291, 815 (1999).

    Article  Google Scholar 

  31. A. Hamiche, Proc. Natl. Acad. Sci. U.S.A. 93, 7588 (1996).

    Article  ADS  Google Scholar 

  32. P.B. Becker, EMBO J. 21, 4749 (2002).

    Article  Google Scholar 

  33. A. Flaus, T. Owen-Hughes, Curr. Opin. Genet. Dev. 14, 165 (2004).

    Article  Google Scholar 

  34. C.J. Brandl, K. Struhl, Mol. Cell. Biol. 10, 4256 (1990).

    Google Scholar 

  35. M. Kanduri, Mol. Cell. Biol. 22, 3339 (2002).

    Article  Google Scholar 

  36. N. Gilbert, J. Allan, Proc. Natl. Acad. Sci. U.S.A. 98, 11949 (2001).

    Article  ADS  Google Scholar 

  37. C. Vaillant, Formation and positioning of nucleosomes: Effect of sequence-dependent long-range correlated structural disorder, this issue, p. 263.

  38. Y.Y. Hsu, Y.H. Wang, J. Biol. Chem. 277, 17315 (2002).

    Article  Google Scholar 

  39. D.T. Kirkpatrick, Mol. Cell. Biol. 19, 7661 (1999).

    Google Scholar 

  40. C. Anselmi, Biophys. J. 79, 601 (2000).

    Article  Google Scholar 

  41. V.G. Levitsky, Nucleic Acids Res. 32 (Web Server issue), W346-9 (2004).

  42. A. Lesne, J.-M. Victor, Chromatin fiber functional organization: Some plausible models, this issue, p. 279.

  43. J. Zlatanova, S.H. Leuba, J. Mol. Biol. 331, 1 (2003).

    Article  Google Scholar 

  44. C. Claudet, J. Bednar, Pulling the chromatin, this issue, p. 331.

  45. T.A. Blank, P.B. Becker, J. Mol. Biol. 252, 305 (1995).

    Article  Google Scholar 

  46. F. Fuks, The view from the biochemist, this issue, p. 367.

  47. A. Benecke, Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs, this issue, p. 353.

  48. Y. Huyen, Nature 432, 406 (2004).

    Article  ADS  Google Scholar 

  49. S. Henikoff, Y. Dalal, Curr. Opin. Genet. Dev. 15, 177 (2005).

    Article  Google Scholar 

  50. E.R. Foster, J.A. Downs, FEBS J. 272, 3231 (2005).

    Article  Google Scholar 

  51. A.S. Belmont, Curr. Opin. Cell. Biol. 11, 307 (1999).

    Article  Google Scholar 

  52. A.S. Belmont, K. Bruce, J. Cell. Biol. 127, 287 (1994).

    Article  Google Scholar 

  53. K. Byrd, V.G. Corces, J. Cell. Biol. 162, 565 (2003).

    Article  Google Scholar 

  54. D. Sproul, N. Gilbert, W.A. Bickmore, Nat. Rev. Genet. 6, 775 (2005).

    Article  Google Scholar 

  55. D. Carter, Nat. Genet. 32, 623 (2002).

    Article  Google Scholar 

  56. P.R. Cook, J. Cell. Sci. 116, 4483 (2003).

    Article  ADS  Google Scholar 

  57. J.R. Swedlow, T. Hirano, Mol. Cell 11, 557 (2003).

    Article  Google Scholar 

  58. B.D. Lavoie, E. Hogan, D. Koshland, J. Cell. Biol. 156, 805 (2002).

    Article  Google Scholar 

  59. S. Almagro, J. Biol. Chem. 279, 5118 (2004).

    Article  Google Scholar 

  60. J.F. Marko, M.G. Poirier, Biochem. Cell. Biol. 81, 209 (2003).

    Article  Google Scholar 

  61. J. Mozziconacci, FEBS Lett. 580, 368 (2006).

    Article  Google Scholar 

  62. T. Cremer, C. Cremer, Nat. Rev. Genet. 2, 292 (2001).

    Article  Google Scholar 

  63. T. Cremer, Biol. Cell 96, 555 (2004).

    Article  Google Scholar 

  64. T. Misteli, Bioessays 27, 477 (2005).

    Article  Google Scholar 

  65. S. Kozubek, Chromosoma 108, 426 (1999).

    Article  Google Scholar 

  66. T. Misteli, Cell 119, 153 (2004).

    Article  Google Scholar 

  67. L. Parada, T. Misteli, Trends Cell. Biol. 12, 425 (2002).

    Article  Google Scholar 

  68. L.A. Parada, P.G. McQueen, T. Misteli, Genome Biol. 5, R44 (2004).

  69. D. Gerlich, Cell 112, 751 (2003).

    Article  Google Scholar 

  70. E.M. Manders, Chromosome Res. 11, 537 (2003).

    Article  Google Scholar 

  71. J. Langowski, Polymer chain models of DNA and chromatin, this issue, p. 241.

  72. G. Li, Nat. Struct. Mol. Biol. 12, 46 (2005).

    Article  Google Scholar 

  73. S. Henikoff, T. Furuyama, K. Ahmad, Trends Genet. 20, 320 (2004).

    Article  Google Scholar 

  74. R. Blossey, Regulating chromatin: On code and dynamic models, this issue, p. 371.

  75. J.-F. Allemand, Loops in DNA: An overview of experimental and theoretical approaches, this issue, p. 293.

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Lavelle, C., Benecke, A. Chromatin physics: Replacing multiple, representation-centered descriptions at discrete scales by a continuous, function-dependent self-scaled model. Eur. Phys. J. E 19, 379–384 (2006). https://doi.org/10.1140/epje/i2005-10059-9

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