Chromatin conformation in living cells: Support for a zig-zag model of the 30 nm chromatin fiber

Journal of Molecular Biology

Volumn 284, Issue 1, 1998, Pages 71-84

  Rydberg, Björn ^a   Holley, William R ^a   Mian, I Saira ^a   Chatterjee, Aloke ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Chromatin fiber; DNA breaks; Ionizing radiation; Nucleosome; Zig zag model

Indexed keywords

DNA FRAGMENT;

ANIMAL CELL; ARTICLE; CALCULATION; CELL CYCLE G0 PHASE; CHO CELL; CHROMATIN STRUCTURE; CONTROLLED STUDY; HUMAN; HUMAN CELL; IONIZING RADIATION; MITOSIS; MOLECULAR MODEL; NONHUMAN; NUCLEOSOME; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; SIMULATION; SKIN FIBROBLAST; X RAY;

EID: 0032553448     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2150     Document Type: Article

References (27)

1. Adolph K. W., Kreisman L. R., Kuehn R. L. Assembly of chromatin fibers into metaphase chromosomes analyzed by transmission electron microscopy and scanning electron microscopy. Biophys. J. 49:1986;221-231.
2. Arents G., Moudrianakis E. N. Topography of the histone octamer surface: repeating structural motifs utilized in the docking of nucleosomal DNA. Proc. Natl Acad. Sci., USA. 90:1993;10489-10493.
3. Burki H. J., Lam C. K., Wood R. D. UV-light-induced mutations in synchronous CHO cells. Mutat. Res. 69:1980;347-356.
4. Bordas J., Perez-Grau L., Koch M. H. J., Vega M. C., Nave C. The superstructure of chromatin and its condensation mechanism II: Theoretical analysis of the X-ray scattering patterns and model calculations. Eur. Biophys. J. 13:1986;175-185.
5. Chatterjee A., Holley W. R. Energy deposition mechanisms and biochemical aspects of DNA strand breaks by ionizing radiation. Int. J. Quant. Chem. 39:1991;709-727.
6. Compton J. L., Bellard M., Chambon P. Biochemical evidence of variability in the DNA Repeat Length in the Chromatin of Higher Eukaryotes. Proc. Natl Acad. Sci. USA. 73:1976;4382-4386.
7. Ferrer P., Caizergues-Ferrer M., Amalric F., Zalta J.-P. Structure of nucleolar and rDNA chromatin in CHO cells. Biol. Cell. 39:1980;155-157.
8. Finch J. T., Klug A. Solenoid model for superstructure in chromatin. Proc. Natl Acad. Sci. USA. 73:1976;1897-1901.
9. Franchet-Beuzit J., Spotheim-Maurizot M., Sabattier R., Blazy-Baudras B., Charlier M. Radiolytic footprinting. β Rays, γ photons & fast neutrons probe DNA-protein interactions. Biochemistry. 32:1993;2104-2110.
10. Henle E. S., Roots R., Holley W. R., Chatterjee A. DNA strand breakage is correlated with unaltered base release after gamma irradiation. Radiat. Res. 143:1995;144-150.
11. Henner W. D., Grunberg S. M., Haseltine W. A. Sites and structure of γ radiation-induced DNA strand breaks. J. Biol. Chem. 257:1982;11750-11754.
12. Holley W. R., Chatterjee A. Clusters of DNA damage induced by ionizing radiation: formation of short DNA fragments. I. Theoretical modeling. Radiat. Res. 145:1996;188-199.
13. Holley W. R., Chatterjee A., Magee J. L. Production of DNA strand breaks by direct effects of heavy charged particles. Radiat. Res. 121:1990;161-168.
14. Horowitz R. A., Agard D. A., Sedat J. W., Woodcock C. L. The three-dimensional architecture of chromatin in situ: electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon. J. Cell Biol. 125:1994;1-10.
15. Luger K., Mader A. W., Richmond R. K., Sargent D. F., Richmond T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature. 389:1997;251-260.
16. Rydberg B. Clusters of DNA damage induced by ionizing radiation: formation of short DNA fragments. II. Experimental detection. Radiat. Res. 145:1996;200-209.
17. Rydberg B., Holley W. R., Chatterjee A. Regionally multiply damaged sites: theoretical and experimental evidence. Fuciarelli A. F., Zimbrick J. D. Radiation Damage in DNA: Structure/Function Relationships at Early Times. 1995;55-63 Battelle Press, Columbus.
18. Sambrook J., Fritsch E. F., Maniatis T. Molecular Cloning: A Laboratory Manual. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
19. Shen X., Yu L., Weir J. W., Gorovsky M. A. Linker histones are not essential and affect chromatin condensation in vivo. Cell. 82:1995;47-56.
20. Swarts S. G., Sevilla M. D., Becker D., Tokar C. J., Wheeler K. T. Radiation-induced DNA damage as a function of hydration. I. Release of unaltered bases. Radiat. Res. 129:1991;333-334.
21. Ward J. F., Kuo I. Deoxynucleotides: models for studying mechanisms of strand breakage in DNA. II. Thymidine 3′5′ diphosphate. Int. J. Radiat. Biol. 23:1973;543-557.
22. Widom J. Toward a unified model of chromatin folding. Annu. Rev. Biophys. Biophys. Chem. 18:1989;365-395.
23. Widom J. Structure of the 300-Å chromatin filament. Adolph K. W. Chromosomes: Eukaryotic, Prokaryotic & Viral. 1990;127-147 CRC Press, Inc. Boca Raton.
24. Widom J. A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells. Proc. Natl Acad. Sci. USA. 89:1992;1095-1099.
25. Woodcock C. L., Frado L.-L. Y., Rattner J. B. The higher-order structure of chromatin: evidence for a helical ribbon arrangement. J. Cell. Biol. 99:1984;42-52.
26. Woodcock C. L., Grigoryev S. A., Horowitz R. A., Whitaker N. A chromatin folding model that incorporates linker variability genetates fibers resembling the native structures. Proc. Natl Acad. Sci. USA. 90:1993;9021-9025.
27. Worcel A., Strogatz S., Riley D. Structure of chromatin and the linking number of DNA. Proc. Natl Acad. Sci. USA. 78:1981;1461-1465.