Chromatin fiber structure and plectonemic model of chromosome condensation in Drosophila cells

DNA and Cell Biology

Volumn 27, Issue 2, 2008, Pages 65-70

  Banfalvi, Gaspar ^a  

^a UNIVERSITY OF DEBRECEN   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

CELL MEMBRANE PERMEABILITY; CELL NUCLEUS; CELL STRUCTURE; CHROMATIN; CHROMATIN CONDENSATION; CHROMOSOME CONDENSATION; COMPUTER ANALYSIS; DROSOPHILA; FLUORESCENCE ANALYSIS; GEOMETRY; KARYOTYPE; NONHUMAN; NUCLEOSOME; PLECTONEMA; PRIORITY JOURNAL; REVIEW;

ANIMALS; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; DROSOPHILA; HUMANS; MODELS, BIOLOGICAL; NUCLEIC ACID CONFORMATION; NUCLEOSOMES; PLECTONEMA;

EID: 39449135611     PISSN: 10445498     EISSN: None     Source Type: Journal    
DOI: 10.1089/dna.2007.0671     Document Type: Review

References (53)

1. Abney, J.R., Cutler, B., Fillbach, M.L., Axelrod, D., and Scalettar, B.A. (1997). Chromatin dynamics in interphase nuclei and its implications for nuclear structure. J Cell Sci 137, 1459-1468.
2. Adolph, K.W. (1980). Organization of chromosomes in HeLa cells: isolation of histone-depleted nuclei and nuclear scaffolds. J Cell Sci 42, 291-304.
3. Adolph, K.W., Cheng, S.M., and Laemmli, U.K. (1977). Role of nonhistone proteins in metaphase chromosome structure. Cell 12, 805-816.
4. Banfalvi, G. (1993). Fluorescent analysis of replication and intermediates of chromatin folding in nuclei of mammalian cells. In Biotechnology Applications of Microinjection, Microscopic Imaging, and Fluorescence. P. Bach, C.H. Reynolds, J.M. Clark, J. Mottley, and P.L. Poole, eds. (Plenum Press, New York), pp. 111-119.
5. Banfalvi, G. (2006). Structure of interphase chromosomes in the nuclei of Drosophila cells. DNA Cell Biol 25, 547-553.
6. Banfalvi, G., Gacsi, M., Nagy, G., Kiss, B.Z., and Basnakian, A.G. (2005). Cadmium induced apoptotic changes in chromatin structure and subphases of nuclear growth during the cell cycle in CHO cells. Apoptosis 10, 631-642.
7. Banfalvi, G., Nagy, G., Gacsi, M., Roszer, T., and Basnakian, A.G. (2006). Common pathway of chromosome condensation in mammalian cells. DNA Cell Biol 25, 295-301.
8. Banfalvi, G., Poirier, L., Mikhilova, M., and Chou, M.V. (1997). Relationship between repair and replicative DNA synthesis to cell cycle in Chinese hamster ovary (CHO-K1) cells. DNA Cell Biol 16, 1155-1160.
9. Banfalvi, G., Sooki-Toth, A., Sarkar, N., Csuzi, S., and Antoni, F. (1984). Nascent DNA synthesized in reversibly permeable cells of mouse thymocytes. Eur J Biochem 139, 553-559.
10. Banfalvi, G., Trencsenyi, G., Ujvarosi, K., Nagy, G., Ombodi, T., Bedei, M., Somogyi, C., and Basnakian, A.G. (2007). Supra-nucleosomal organization of chromatin fibers in nuclei of Drosophila S2 cells. DNA Cell Biol 26, 55-62.
11. 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 histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc Natl Acad Sci USA 95, 14173-14178.
12. Benyajati, C., and Worcel, A. (1976). Isolation, characterization and structure of the folded interphase genome of Drosophila melanogaster. Cell 9, 393-400.
13. Berezney, R., Mortillaro, M.J., Ma, H., Wei, X., and Samarabandu, J. (1995). The nuclear matrix: a structural milieu for genomic function. Int Rev Cytol 162A, 1-65.
14. Bordas, J., Perez-Grau, L., Koch, M.H.J., Vega, M.C., and Nave, C. (1986). The superstructure of chromatin and its condensation mechanism. I. Synchrotron radiation X-ray scattering results. Eur Biophys J Biophys Lett 13, 175-185.
15. Castellot, J.J., Jr., Miller, M.R., and Pardee, A.B. (1978). Animal cells reversibly permeable to small molecules. Proc Natl Acad Sci USA 75, 351-355.
16. Comings, D.E. (1980). Arrangement of chromatin in the nucleus. Hum Genet 53, 131-143.
17. Cook, P.R., and Brazell, I.A. (1980). Mapping sequences in loops of nuclear DNA by their progressive detachment from the nuclear cage. Nucleic Acids Res 8, 2895-2907.
18. Cremer, C., Cremer, T., Zorn, C., and Cioreanu, V. (1979). Partial irradiation of Chinese hamster cell nuclei and detection of unscheduled DNA synthesis in interphase and metaphase. A tool to investigate the arrangement of interphase chromosomes in mammalian cells. Hoppe-Seyler's Z Physiol Chem 360, 244-245.
19. Cremer, T., and Cremer, C. (2001). Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2, 292-301.
20. Cremer, T., Cremer, M., Dietzel, S., Müller, S., Solovei, I., and Fakan, S. (2006). Chromosome territories - a functional nuclear landscape. Curr Opin Cell Biol 18, 307-316.
21. Dietzel, S., and Belmont, A.S. (2001). Reproducible but dynamic positioning of DNA within chromosomes during mitosis. Nat Cell Biol 3, 767-770.
22. Earnshaw, W., and Laemmli, U.K. (1983). Architecture of metaphase chromosomes and chromosome scaffolds. J Cell Biol 96, 84-93.
23. Earnshaw, W.C. (1988). Mitotic chromosome structure. Bioessays 9, 147-150.
24. Finch, J.T., and Klug, A. (1976). Solenoidal model for super-structure in chromatin. Proc Natl Acad Sci USA 73, 1897-1901.
25. Grechman, S.E., and Ramakrishnan, V. (1987). Chromatin higher-order structure studied by neutron-scattering and scanning transmission electron microscopy. Proc Natl Acad Sci USA 84, 7802-7806.
26. Grigoryev, S.A. (2004). Keeping fingers crossed: heterochromatin spreading through interdigitation of nucleosome arrays. FEBS Lett 254, 4-8.
27. Heslop-Harrison, J.S., Huelskamp, M., Wendroth, S., Atkinson, M.D., Leicht, A.R., and Benett, M.D. (1988). Chromatin and centromeric structures in interphase nuclei. In Kew Chromosome Conference III. P.E. Brandham, ed. (Allen & Unwin, London), pp. 209-217.
28. Hozak, P., and Fakan, S. (2006). Functional structure of the cell nucleus. Histochem Cell Biol 125, 1-2.
29. Kireeva, N., Lakonishok, M., Kireev, I., Hirano, T., and Belmont, A.S. (2004). Visualization of early chromosome condensation: a hierarchical folding, axial glue model of chromosome structure. J Cell Biol 166, 775-785.
30. Kosak, S.T., and Groudine, M. (2004). Form follows function: the genomic organization of cellular differentiation. Genes Dev 18, 1371-1384.
31. Kubista, M., Hagmar, P., Nielsen, P.E., and Nordén, B. (1990). Reinterpretation of linear dichroism of chromatin supports a perpendicular linker orientation in the folded state. J Biomol Struct Dyn 8, 37-54.
32. Luger, K. (2003). Structure and dynamic behavior of nucleosomes. Curr Opin Genet Dev 13, 127-135.
33. Manuelidis, L. (1990). A view of interphase chromosomes. Science 250, 1533-1540.
34. Moses, R.E., and Richardson, C.C. (1970). Replication and repair of DNA in cells of Escherichia coli treated with toluene. Proc Natl Acad Sci USA 67, 674-681.
35. Nagy, G., Gacsi, M., Rehak, M., Basnakian, A.G., Klaisz, M., and Banfalvi, G. (2004). Gamma irradiation-induced apoptosis in murine pre-B cells prevents the condensation of fibrillar chromatin in early S phase. Apoptosis 9, 765-776.
36. Parada, L.A., McQueen, P., and Misteli, T. (2004). Tissue-specific spatial organization of genomes. Genome Biol 5, R44.
37. Parada, L.A., and Misteli, T. (2002). Chromosome positioning in the interphase nucleus. Trends Cell Biol 12, 425-432.
38. Paulson, J.R., and Laemmli, U.K. (1977). The structure of histone-depleted metaphase chromosomes. Cell 12, 817-828.
39. Pederson, T. (2004). The spatial organization of the genome in mammalian cells. Curr Opin Genet Dev 14, 203-209.
40. Rydberg, B., Holley, W.R., Mian, I.S., and Chatterjee, A. (1998). Chromatin conformation in living cells: support for a zigzag model of the 30nm chromatin fiber. J Mol Biol 284, 71-84.
41. Sperling, K., and Luedtke, E.-K. (1981). Arrangement of prematurely condensed chromosomes in cultured cells and lymphocytes of the Indian muntjac. Chromosoma 83, 541-553.
42. Sun, J., Zhang, Q., and Schlick, T. (2005). Electrostatic mechanism of nucleosomal array folding revealed by computer simulation. Proc Natl Acad Sci USA 102, 8180-8185.
43. Ujvarosi, K., Hunyadi, J., Nagy, G., Pocsi, I., and Banfalvi, G. (2007). Preapoptotic chromatin changes induced by ultraviolet B irradiation in human erythroleukemia K562 cells. Apoptosis 12, 2089-2097.
44. Van Driel, R., Fransz, P.F., and Verschure, P.J. (2003). The eukaryotic genome: a system regulated at different hierarchical levels. J Cell Sci 116, 4067-4075.
45. Van Holde, K., and Zlatanova, J. (1996). What determines the folding of the chromatin fiber? Proc Natl Acad Sci USA 93, 10548-10555.
46. Widom, J. (1998). Structure, dynamics, and function of chromatin in vitro. Annu Rev Biophys Biomol Struct 27, 285-327.
47. Williams, S.P., Athey, B.D., Muglia, L.J., Schappe, R.S., Gough, A.H., and Langmore, J.P. (1986). Chromatin fibers are left-handed double helices with diameter and mass per unit length that depend on linker length. Biophys J 49, 233-248.
48. Woodcock, C.L., Frado, L.L., and Rattner, J.B. (1984). The higher-order structure of chromatin: evidence for a helical ribbon arrangement. J Cell Biol 99, 42-52.
49. 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 USA 90, 9021-9025.
50. Woodcock, C.L., and Horowitz, L.A. (1997). Electron microscopy of chromatin. Methods 12, 84-95.
51. Woodcock, C.L., and Horowitz, R.A. (1995). Chromatin organization re-viewed. Trends Cell Biol 5, 272-277.
52. Worzel, A., Strogatz, A., and Riley, D. (1981). Structure of chromatin and the linking number of DNA. Proc Natl Acad Sci USA 78, 1461-1465.
53. Zlatanova, J., Leuba, S.H., and van Holde, K. (1998). Chromatin fiber structure: morphology, molecular determinants, structural transitions. Biophys J 74, 2554-2566.