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The superstructure of chromatin and its condensation mechanism

VI. Electric dichroism and model calculations

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Abstract

Electric dichroism and X-ray scattering measurements on solutions of uncondensed and condensed chicken erythrocyte chromatin were interpreted on the basis of model calculations. Information about the state of uncondensed fibers in the conditions of electric dichroism measurements was obtained from scattering patterns recorded as a function of pH, in the presence of spermine and at very low monovalent cation concentrations. Electric dichroism measurements on a complex of uncondensed chromatin with methylene blue were made to determine the contribution of the linker and of the nucleosomes to the total dichroism.

A new approach to calculate the dichroism from realistic structural models, which also yields other structural parameters (radius of gyration, radius of gyration of the cross-section, mass per unit length) was used. Only a restricted range of structures is simultaneously compatible with all experimental results. Further, it is shown that previous interpretations of dichroism measurements on chromatin were in contradiction with X-ray scattering data and failed to take into account the distribution of orientation of the nucleosomes in the fibers. When this is done, it is found that the linker DNA in chicken erythrocyte and sea urchin chromatin must run nearly perpendicularly to the fibre axis. Taken together with the dependence of the fibre diameter on the linker length, these results provede the strongest evidence hitherto available for a model in which the linker crosses the central part of the fibre.

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References

  • Angerer LM, Moudrianakis EN (1972) Interaction of ethidium bromide with whole and selectively deproteinized deoxynucleoproteins from calf thymus. J Mol Biol 63:505–521

    Google Scholar 

  • Ausio J, Borochov N, Seger D, Eisenberg H (1984) Interaction of chromatin with NaCl and MgCl2: Solubility and binding studies, transition to and characterization of the higher order structure. J Mol Biol 177:373–398

    Google Scholar 

  • Bordas J, Perez-Grau L, Koch MHJ, Nave C, Vega MC (1986) The superstructure of chromatin and its condensation mechanism. I: Synchrotron radiation X-ray scattering results. Eur Biophys J 13:157–174

    Google Scholar 

  • Boulin C, Kempf R, Koch MHJ, McLaughlin SM (1986) Data appraisal, evaluation and display for synchrotron radiation experiments: hardware and software. Nucl Instrum Methods A 249:399–407

    Google Scholar 

  • Boulin CJ, Kempf R, Gabriel A, Koch MHJ (1988) Data acquisition systems for linear and area X-ray detectors using delay line readout. Nucl instrum Methods A 269:312–320

    Google Scholar 

  • Buche A, Ouassaidi A, Hacha R, Delpire E, Gilles R, Houssier C (1989) Glycine and other amino-organic compounds prevent chromatin precipitation at physiological ionic strength. FEBS Lett 247:367–370

    Google Scholar 

  • Butler PJG (1984) A defined structure of the 30-nm chromatic fibre which accommodates different nucleosomal repeat lengths. EMBO J 3:2599–2604

    Google Scholar 

  • Butler PJG (1988) The organization of the chromatin fibre. In: Adolph KW (ed) Chromosomes and chromatin, I. CRC Press, Boca Raton, pp 57–82

    Google Scholar 

  • Cantor CR, Schimmel PR (1980). Biophysical chemistry, Freeman, San Francisco

    Google Scholar 

  • Chauvin F, Roux B, Marion C (1985) Higher order structure of chromatin: influence of ionic strength and proteolytic digestion on the birefringence properties of polynucleosomal fibres. J Biomol Struct Dyn 2:805–819

    Google Scholar 

  • Dimitrov SI, Smirnov IV, Makarov VL (1988) Optical anisotropy of chromatin: Flow linear dichroism and electric dichroism studies. J Biomol Struct Dyn 5:1135–1148

    Google Scholar 

  • Finch JT, Klug A (1976) Solenoidal model for superstructure in chromatin. Proc Natl Acad Sci USA 73:1897–1901

    Google Scholar 

  • Fredericq E, Houssier C (1973) Electric dichroism and electric birefringence. Clarendon Press, Oxford

    Google Scholar 

  • Genest D, Sabeur G, Wahl P, Auchet J-C (1981) Fluorescence anisotropy decay of ethidium bound to chromatin. Biophys Chem 13:77–87

    Google Scholar 

  • Hagmar P, Marquet R, Colson P, Kubista M, Nielsen P, Norden B, Houssier C (1989) Electric flow and linear dichroism of unfolded and condensed chromatin: A comparative study at low and intermediate ionic strength. J Biomol Struct Dyn 7:19–27

    Google Scholar 

  • Harrington RE (1985) Optical model studies of the salt induced 10–30-nm fiber transition in chromatin. Biochemistry 24: 2011–2021

    Google Scholar 

  • Koch MHJ (1989) Structure and condensation of chromatin. In: Saenger W, Heinemann U (eds) Protein—Nucleic acid interactions. McMillan, London, pp 163–204

    Google Scholar 

  • Koch MHJ, Bordas J (1983) X-ray diffraction and scattering on disordered systems using synchrotron radiation. Nucl Instrum Methods 208:461–469

    Google Scholar 

  • Koch MHJ, Vega MC, Sayers Z, Michon AM (1987a) The superstructure of chromatin and its condensation mechanism. III: Effect of monovalent and divalent cations X-ray solution scattering and hydrodynamic studies. Eur Biophys J 14:307–319

    Google Scholar 

  • Koch MHJ, Sayers Z, Vega MC, Michon AM (1987b) The superstructure of chromatin and its condensation mechanism. IV: Enzymatic digestion, thermal denaturation, effect of netropsin and distamycin. Eur Biophys J 15:133–140

    Google Scholar 

  • Koch MHJ, Sayers Z, Michon AM, Marquet R, Houssier C, Willführ J (1988) The superstructure of chromatin and its condensation mechanism. V: Effect of linker length, condensation by multivalent cations, solubility and electric dichroism properties. Eur Biophys J 16:177–185

    Google Scholar 

  • Kubista M, Hard T, Nielsen PE, Norden B (1985) Structural transitions of chromatin at low salt concentrations: A flow linear dichroism study. Biochemistry 24:6336–6342

    Google Scholar 

  • Lee KS, Mandelkern M, Crothers DM (1981) Solution structural studies of chromatin fibers. Biochemistry 20:1438–1445

    Google Scholar 

  • McGhee JD, Rau DC, Charney E, Felsenfeld G (1980) Orientation of the nucleosome within the higher order structure of chromatin. Cell 22:87–96

    Google Scholar 

  • McGhee JD, Nickol JM, Felsenfeld G, Rau DC (1983) Higher order structure of chromatin, orientation of nucleosomes within the 30 nm chromatin solenoid is independent of species and spacer length. Cell 33:831–841

    Google Scholar 

  • Marquet R, Houssier C, Fredericq E (1985) An electro-optical study of the mechanisms of DNA condensation induced by spermine. Biochim Biophys Acta 825:365–374

    Google Scholar 

  • Marquet R, Colson P, Matton AM, Houssier C, Thiry M, Goessens G (1988) Comparative study of the condensation of chicken erythrocyte and calf thymus chromatins by di- and multivalent cations. J Biomol Struct Dyn 5:839–857

    Google Scholar 

  • Norden B, Tjerneld F (1982) Structure of methylene blue DNA complexes studied by linear and circular dichroism spectroscopy. Biopolymers 21:1713–1734

    Google Scholar 

  • Paoletti J, Magee BB, Magee PT (1977) The structure of chromatin: interaction of ethidium bromide with native and denatured chromatin. Biochemistry 16:351–357

    Google Scholar 

  • Porschke D (1985) Short electric field pulses convert DNA from “condensed” to “free” conformation. Biopolymers 23:4821–4828

    Google Scholar 

  • Richmond TJ, Finch JT, Rushton B, Rhodes D, Klug A (1984) Structure of the nucleosome core particle at 7 Å resolution. Nature 311:532–537

    Google Scholar 

  • Sayers Z (1988) Synchrotron X-ray scattering studies of the chromatin fibre structure. In: Mandelkow E (ed) Synchrotron radiation in chemistry and biology I. Topics in Current Chemistry, vol 145. Springer, Berlin Heidelberg New York, pp 203–232

    Google Scholar 

  • Sen D, Crothers DM (1986) Condensation of chromatin: Role of multivalent cations. Biochemistry 25:1495–1503

    Google Scholar 

  • Sen D, Mitra S, Crothers DM (1986) Higher order structure of chromatin: Evidence of photochemically detected linear dichroism. Biochemistry 25:3441–3447

    Google Scholar 

  • Suau P, Kneale GG, Braddock GW, Baldwin JP, Bradbury EM (1977) A low resolution model for the chromatin core particle by neutron scattering. Nucleic Acids Res 4:3769–3786

    Google Scholar 

  • Tanford C (1961) Physical chemistry of macromolecules. Wiley, New York

    Google Scholar 

  • Thoma F, Koller T, Klug A (1979) Involvement of histone H1 in the organization of the nucleosome and of the salt dependent superstructures of chromatin. J Cell Biol 83:403–407

    Google Scholar 

  • Tjerneld F, Norden B, Wallin H (1982) Chromatin structure studied by linear dichroism at different salt concentrations. Biopolymers 21:343–358

    Google Scholar 

  • Widom J (1986) Physicochemical studies of the folding of the 100 Å nucleosome filament into the 300 Å filament. J Mol Biol 190:411–424

    Google Scholar 

  • Widom J, Klug A (1985) Structure of the 300 Å filament: X-ray diffraction from oriented samples. Cell 43:207–213

    Google Scholar 

  • Williams SP, Athey BD, Muglia LJ, Schappe R, Gough AJ, Langmore JP (1986) Chromatin fibres are left-handed double helices with diameter and mass per unit length that depend on linker length. Biophys J 49:233–250

    Google Scholar 

  • Yabuki H, Dattagupta N, Crothers DM (1982) Orientation of nucleosomes in the thirty-nanometer chromatin fiber. Biochemistry 21:5051–5020

    Google Scholar 

Download references

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Authors and Affiliations

  1. European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, D-2000, Hamburg 52, Federal Republic of Germany

    M. H. J. Koch, Z. Sayers, A. M. Michon & P. Sicre

  2. Laboratoire de Chimie Macromoléculaire et Chimie Physique, Sart tilman (B6), Université de Liège, B-4000, Liège, Belgium

    R. Marquet & C. Houssier

Authors
  1. M. H. J. Koch
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  2. Z. Sayers
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  3. A. M. Michon
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  4. P. Sicre
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  5. R. Marquet
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  6. C. Houssier
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Koch, M.H.J., Sayers, Z., Michon, A.M. et al. The superstructure of chromatin and its condensation mechanism. Eur Biophys J 17, 245–255 (1989). https://doi.org/10.1007/BF00254282

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  • DOI: https://doi.org/10.1007/BF00254282

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