High concentration of DNA in condensed chromatin

Biochemistry and Cell Biology

Volumn 81, Issue 3, 2003, Pages 91-99

  Daban, Joan Ramon ^a  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

Chromatin; Chromatin higher order structure; Chromosomes; DNA; Metaphase chromosomes

Indexed keywords

CHROMOSOMES; DNA; MOLECULAR BIOLOGY;

MITOSIS;

CELL CULTURE;

CALCIUM ION; DNA; MAGNESIUM ION;

CHROMATID; CHROMATIN CONDENSATION; CONCENTRATION (PARAMETERS); CONFERENCE PAPER; DNA DETERMINATION; EUKARYOTIC CELL; GENOME; HUMAN; METAPHASE; MITOSIS; MODEL; NONHUMAN; NUCLEOSOME;

ANIMALS; CALCIUM; CHROMATIN; DNA; HUMANS; MAGNESIUM; MODELS, MOLECULAR; NUCLEOSOMES;

EUKARYOTA; SOLENOIDEA;

EID: 0042733701     PISSN: 08298211     EISSN: None     Source Type: Journal    
DOI: 10.1139/o03-037     Document Type: Conference Paper

References (91)

1. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., and Walter, P. 2002. Molecular biology of the cell. Garland Science, New York.
2. Arents, G., Burlingame, R.W., Wang, B.-C., Love, W.E., and Moudrianakis, E.N. 1991. The nucleosomal core histone octamer at 3.1 Å resolution: A tripartite protein assembly and a left-handed superhelix. Proc. Natl. Acad. Sci. U.S.A. 88: 10 148-10 152.
3. 2: Solubility and binding studies, transition to and characterization of the higher-order structure. J. Mol. Biol. 177: 373-398.
4. Ausió, J., Abbott, D.W., Wang, X., and Moore, S.C. 2001. Histone variants and histone modifications: A structural perspective. Biochem. Cell Biol. 79: 693-708.
5. Bak, A.L., Zeuthen, J., and Crick, F.H.C. 1977. Higher-order structure of human mitotic chromosomes. Proc. Natl. Acad. Sci. U.S.A. 74: 1595-1599.
6. Bartolomé, S., Bermúdez, A., and Daban, J.-R. 1994. Internal structure of the 30 nm chromatin fiber. J. Cell Sci. 107: 2983-2992.
7. 2+: Self-assembly of small chromatin fragments and folding of the 30-nm fiber. J. Biol. Chem. 270: 22 514-22 521.
8. Bednar, J., Horowitz, R.A., Grigoryev, S.A., Carruthers, L.M., Hansen, J.C., Koster, A.J., and Woodcock, C.L. 1998. Nucleosomes, linker DNA, and linker histones form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc. Natl. Acad. Sci. U.S.A. 95: 14 173-14 178.
9. Belmont, A.S., and Bruce, K. 1994. Visualization of G1 chromosomes: A folded, twisted, supercoiled chromonema model of interphase chromatid structure. J. Cell Biol. 127: 287-302.
10. Belmont, A.S., Sedat, J.W., and Agard, D.A. 1987. A three-dimensional approach to mitotic chromosome structure: Evidence for a complex hierarchical organization. J. Cell Biol. 105: 77-92.
11. Bennett, M.D., Heslop-Harrison, J.S., Smith, J.B., and Ward, J.P. 1983. DNA density in mitotic and meiotic metaphase chromosomes of plants and animals. J. Cell Sci. 63: 173-179.
12. Bermúdez, A., Bartolomé, S., and Daban, J.-R. 1998. Partial denaturation of small chromatin fragments: Direct evidence for the radial distribution of nucleosomes in folded fibers. J. Cell Sci. 111: 1707-1715.
13. Bohrmann, B., Haider, M., and Kellenberger, E. 1993. Concentration evaluation of chromatin in unstained resin-embedded sections by means of low-dose ratio-constrast imaging in STEM. Ultramicroscopy, 49: 235-251.
14. Booy, F.P., Newcomb, W.W., Trus, B.L., Brown, J.C., Baker, T.S., and Steven, A.C. 1991. Liquid-crystalline, phage-like packing of encapsidated DNA in herpes simplex virus. Cell, 64: 1007-1015.
15. Bordas, J., Perez-Grau, L., Koch, M.H.J., Vega, M.C., and Nave, C. 1986. The superstructure of chromatin and its condensation mechanism: II. Theoretical analysis of the X-ray scattering patterns and model calculations. Eur. Biophys. J. 13: 175-185.
16. Boy de la Tour, E., and Laemmli, U.K. 1988. The metaphase scaffold is helically folded: Sister chromatids have predominantly opposite helical handedness. Cell, 55: 937-944.
17. Bradbury, E.M. 2002. Chromatin structure and dynamics: State-of-the-art. Mol. Cell, 10: 13-19.
18. Cantor, C.R., and Schimmel, P.R. 1980. Biophysical chemistry. Freeman, San Francisco.
19. Carruthers, L.M., Bednar, J., Woodcock, C.L., and Hansen, J.C. 1998. Linker histones stabilize the intrinsic salt-dependent folding of nucleosomal arrays. Mechanistic ramifications for higher-order chromatin folding. Biochemistry, 37: 14 776-14 787.
20. Daban, J.-R. 2000. Physical constraints in the condensation of eukaryotic chromosomes: Local concentration of DNA versus linear packing ratio in higher order chromatin structures. Biochemistry, 39: 3861-3866.
21. Daban, J.-R., and Bermúdez, A. 1998. Interdigitated solenoid model for compact chromatin fibers. Biochemistry, 37: 4299-4304.
22. Davey, C.A., and Richmond, T.J. 2002. DNA-dependent divalent cation binding in the nucleosome core particle. Proc. Natl. Acad. Sci. U.S.A. 99: 11 169-11 174.
23. Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W., and Richmond, T.J. 2002. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J. Mol. Biol. 319: 1097-1113.
24. Dubochet, J., and Noll, M. 1978. Nucleosome arcs and helices. Science (Washington, D.C.), 202: 280-286.
25. Earnshaw, W.C., and Laemmli, U.K. 1983. Architecture of metaphase chromosomes and chromosome scaffolds. J. Cell Biol. 96: 84-93.
26. Filipski, J., Leblanc, J., Youdale, T., Sikorska, M., and Walker, P.R. 1990. Periodicity of DNA folding in higher order chromatin structures. EMBO J. 9: 1319-1327.
27. Finch, J.T., Lutter, L.C., Rhodes, D., Brown, R.S., Rushton, B., Levitt, M., and Klug, A. 1977. Structure of nucleosome core particles of chromatin. Nature (London), 269: 29-36.
28. Fritzsche, W., and Henderson, E. 1996. Volume determination of human metaphase chromosomes by scanning force microscopy. Scanning Microsc. 10: 103-110.
29. Graziano, V., Gerchman, S.E., Schneider, D.K., and Ramakrishnan, V. 1994. Histone H1 is located in the interior of the chromatin 30-nm filament. Nature (London), 368: 351-354.
30. Green, G.R., and Poccia, D.L. 1985. Phosphorylation of sea urchin sperm H1 and H2B histones precedes chromatin decondensation and H1 exchange during pronuclear formation. Dev. Biol. 108: 235-245.
31. Greyling, H.J., Schwager, S., Swell, B.T., and von Holt, C. 1983. The identity of conformational states of reconstituted and native histone octamers. Eur. J. Biochem. 137: 221-226.
32. Hansen, J.C. 2002. Conformational dynamics of the chromatin fiber in solution: Determinants, mechanisms, and functions. Annu. Rev. Biophys. Biomol. Struct. 31: 361-392.
33. Harp, J.M., Hanson, B.L., Timm, D.E., and Bunick, G.J. 2000. Asymmetries in the nucleosome core particle at 2.5 Å resolution. Acta Crystallogr. D, 56: 1513-1534.
34. Heslop-Harrison, J.S., Leitch, A.R., Schwarzacher, T., Smith, J.B., Atkinson, M.D., and Bennett, M.D. 1989. The volumes and morphology of human chromosomes in mitotic reconstructions. Hum. Genet. 84: 27-34.
35. International Human Genome Squencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature (London), 409: 860-921.
36. Kellenberger, E., Carlemalm, E., Sechaud, J., Ryter, A., and de Haller, G. 1986. Considerations on the condensation and degree of compactness in non-eukaryotic DNA-containing plasmas. In Bacterial chromatin. Edited by C.O. Gualerzi and C.L. Pon. Springer-Verlag, Berlin. pp. 11-25.
37. Klug, A., Rhodes, D., Smith, J., Finch, J.T., and Thomas, J.O. 1980. A low resolution structure of the histone core of the nucleosome. Nature (London), 287: 509-516.
38. Koch, M.H.J. 1989. Structure and condensation of chromatin. In Protein-Nucleic Acid Interaction. Edited by W. Saenger and U. Heinemann. McMillan Press, London. pp. 163-204.
39. Koch, M.H.J., Vega, M.C., Sayers, Z., and Michon, A.M. 1987. 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.
40. Leforestier, A., and Livolant, F. 1997. Liquid crystalline ordering of nucleosome core particles under macromolecular crowding conditions: Evidence for a discotic columnar hexagonal phase. Biophys. J. 73: 1771-1776.
41. Leforestier, A., Fudaley, S., and Livolant, F. 1999. Spermidine-induced aggregation of nucleosome core particles: Evidence for multiple liquid crystalline phases. J. Mol. Biol. 290: 481-494.
42. Leforestier, A., Dubochet, J., and Livolant, F. 2001. Bilayers of nucleosome core particles. Biophys. J. 81: 2414-2421.
43. Lerman, L.S., Wilkerson, L.S., Venable, J.H., and Robinson, B.H. 1976. DNA packing in single crystals inferred from freeze-fracture-etch replicas. J. Mol. Biol. 108: 271-293.
44. Leuba, S.H., Yang, G., Robert, C., Samori, B., van Holde, K., Zlatanova, J., and Bustamante, C. 1994. Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy. Proc. Natl. Acad. Sci. U.S.A. 91: 11 621-11 625.
45. Lever, M.A., Th'ng, J.P.H., Sun, X., and Hendzel, M.J. 2000. Rapid exchange of histone H1.1 on chromatin in living human cells. Nature (London), 408: 873-876.
46. Lewin, B. 2000. Genes VII. Oxford University Press, Oxford.
47. Livolant, F., and Leforestier, F. 2000. Chiral discotic columnar germs of nucleosome core particles. Biophys. J. 78: 2716-2729.
48. Luger, K., Mäder, A.W., Richmond, R.K., Sargent, D.F., and Richmond, T.J. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature (London), 389: 251-260.
49. Makarov, V., Dimitrov, S., Smirnov, V., and Pashev, I. 1985. A triple helix model for the structure of chromatin fiber. FEBS Lett. 181: 357-361.
50. Manuelidis, L., and Chen, T.L. 1990. A unified model of eukaryotic chromosomes. Cytometry, 11: 8-25.
51. McDowall, A.W., Smith, J.M., and Dubochet, J. 1986. Cryo-electron microscopy of vitrified chromosomes in situ. EMBO J. 5: 1395-1402.
52. Misteli, T., Gunjan, A., Hock, R., Bustin, M., and Brown, D.T. 2000. Dynamic binding of histone H1 to chromatin in living cells. Nature (London), 408: 877-881.
53. Morton, N.E. 1991. Parameters of the human genome. Proc. Natl. Acad. Sci. U.S.A. 88: 7474-7476.
54. Park, J.-H., Cosgrove, M.S., Youngman, E., Wolberger, C., and Boeke, J.D. 2002. A core nucleosome surface crucial for transcriptional silencing. Nature Genetics, 32: 273-279.
55. Paulson, J.R., and Laemmli, U.K. 1977. The structure of histone-depleted metaphase chromosomes. Cell, 12: 817-828.
56. Pienta, K.J., and Coffey, D.S. 1984. A structural analysis of the role of the nuclear matrix and DNA loops in the organization of the nucleus and chromosome. J. Cell Sci. Suppl. 1: 123-135.
57. Pogany, G.C., Corzett, M., Weston, S., and Balhorn, R. 1981. DNA and protein content of mouse sperm. Exp. Cell Res. 136: 127-136.
58. Poirier, M.G., Monhait, T., and Marko, J.F. 2002. Reversible hypercondensation and decondensation of mitotic chromosomes studied using combined chemical-micromechanical techniques. J. Cell. Biochem. 85: 422-434.
59. Rattner, J.B., and Lin, C.C. 1985. Radial loops and helical coils coexist in metaphase chromosomes. Cell, 42: 291-296.
60. Renz, M., Nehls, P., and Hozier, J. 1977. Involvemet of histone H1 in the organization of the chromosome fiber. Proc. Natl. Acad. Sci. U.S.A. 74: 1879-1883.
61. Saitoh, Y., and Laemmli, U.K. 1994. Metaphase chromosome structure: Bands arise from differential folding path of the highly AT-rich scaffold. Cell, 76: 609-622.
62. Schulz, G.E., and Schirmer, R.H. 1979. Principles of protein structure. Springer-Verlag, New York.
63. Sedat, J., and Manuelidis, L. 1978. A direct approach to the structure of eukaryotic chromosomes. Cold Spring Harbor Symp. Quant. Biol. 42: 331-350.
64. Sperling, R., and Wachtel, E.J. 1981. The histones. Adv. Protein Chem. 34: 1-60.
65. Strahl, B.D., and Allis, C.D. 2000. The language of covalent histone modifications. Nature (London), 403: 41-45.
66. Strick, R., Strissel, P.L., Gavrilov, K., and Levi-Setti, R. 2001. Cation chromatin binding as shown by ion microscopy is essential for the structural integrity of chromosomes. J. Cell Biol. 155: 899-910.
67. Subirana, J.A., Muñoz-Guerra, S., Aymamí, J., Radermacher, M., and Frank, J. 1985. The layered organization of nucleosomes in 30 nm chromatin fibers. Chromosoma, 91: 377-390.
68. Sumner, A.T. 2003. Chromosomes: Organization and function. Blackwell Publishing, Oxford.
69. Sun, Z.-W., and Allis, C.D. 2002. Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature (London), 418: 104-108.
70. Suzuki, M., and Wakabayashi, T. 1988. Packaging of DNA in cricket sperm: A compact mode of DNA packaging. J. Mol. Biol. 204: 653-661.
71. Taniguchi, T., and Takayama, S. 1986. Higher-order structure of metaphase chromosomes: Evidence for a multiple coiling model. Chromosoma, 93: 511-514.
72. Tatchell, K., and van Holde, K.E. 1978. Compact oligomers and nucleosome phasing. Proc. Natl. Acad. Sci. U.S.A. 75: 3583-3587.
73. Thoma, F., Koller, Th., and 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: 403-427.
74. Thomas, J.O., and Kornberg, R.D. 1975. An octamer of histones in chromatin and free in solution. Proc. Natl. Acad. Sci. U.S.A. 72: 2626-2630.
75. Uberbacher, E.C., and Bunick, G.J. 1985. X-ray structure of nucleosome core particle. J. Biomol. Struct. Dyn. 2: 1033-1055.
76. van Holde, K., and Zlatanova, J. 1995. Chromatin higher order structure: Chasing a mirage? J. Biol. Chem. 270: 8373-8376.
77. White, C.L., Suto, R.K., and Luger, K. 2001. Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. EMBO J. 20: 5207-5218.
78. 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.
79. Widom, J. 1989. Toward a unified model of chromatin folding. Annu. Rev. Biophys. Biophys. Chem. 18: 365-395.
80. Widom, J. 1998. Structure, dynamics and function of chromatin in vitro. Annu. Rev. Biophys. Biomol. Struct. 27: 285-327.
81. Widom, J., and Klug, A. 1985. Structure of the 300 Å chromatin filament: X-ray diffraction from oriented samples. Cell, 43: 207-213.
82. Williams, S.P., Athey, B.D., Muglia, L.J., Schappe, R.S., Glough, A.H., and Langmore, J.P. 1986. Chromatin fibers are left-handed double helices with diameter and mass per unit length that depends on linker length. Biophys. J. 49: 233-248.
83. Wolffe, A. 1998. Chromatin structure and function. Academic Press, London.
84. Woodcock, C.L., and Dimitrov, S. 2001. Higher-order structure of chromatin and chromosomes. Curr. Opin. Gen. Dev. 11: 130-135.
85. Woodcock, C.L., and Horowitz, R.A. 1997. Electron microscopy of chromatin. Methods, 12: 84-95.
86. Woodcock, C.L.F., Frado, L.-L.Y, and Rattner, J.B. 1984. The higher-order structure of chromatin: Evidence for a helical ribbon arrangement. J. Cell. Biol. 99: 42-52.
87. Woodcock, C.L., Grigoryev, S.A., Horowitz, R.A., and Whitaker, N. 1993. A chromatin folding model that incorporates linker variability generates fibers resembling the native structures. Proc. Natl. Acad. Sci. U.S.A. 90: 9021-9025.
88. Yang, G., Leuba, S.H., Bustamante, C., Zlatanova, J., and van Holde, K. 1994. Role of linker histones in extended chromatin fibre structure. Nature Struct. Biol. 1: 761-763.
89. Zentgraf, H., and Franke, W.W. 1984. Differences of supranucleosomal organization in different kinds of chromatin: Cell type-specific globular subunits containing different numbers of nucleosomes. J. Cell Biol. 99: 272-286.
90. Zlatanova, J., Leuba, S.H., Yang, G., Bustamante, C., and van Holde, K. 1994. Linker DNA accessibility in chromatin fibers of different conformations: A reevaluation. Proc. Natl. Acad. Sci. U.S.A. 91: 5277-5280.
91. Zlatanova, J., Leuba, S.H., and van Holde, K. 1998. Chromatin fiber structure: Morphology, molecular determinants, structural transitions. Biophys. J. 74: 2554-2566.