X-ray structure of a tetranucleosome and its implications for the chromatin fibre

Nature

Volumn 436, Issue 7047, 2005, Pages 138-141

  Schalch, Thomas ^a   Duda, Sylwia ^a   Sargent, David F ^a   Richmond, Timothy J ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL STRUCTURE; DNA; GENETIC ENGINEERING; MATHEMATICAL MODELS; MOLECULAR STRUCTURE; SUBSTRATES; X RAY ANALYSIS;

CHROMATIN FIBERS; NUCLEOSOMES; OLIGONUCLEOSOME; TETRANUCLEOSOME;

CHROMOSOMES;

DNA; HISTONE;

BIOLOGY;

ARTICLE; CELL STRUCTURE; CHROMATIN; CHROMOSOME; CROSS LINKING; CRYSTAL STRUCTURE; DNA POLYMORPHISM; DNA RECOMBINATION; DNA REPAIR; DNA REPLICATION; DNA TRANSCRIPTION; EUKARYOTIC CELL; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; STRUCTURE ANALYSIS; TETRANUCLEOSOME; X RAY ANALYSIS; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENETICS; METABOLISM; X RAY CRYSTALLOGRAPHY; XENOPUS LAEVIS;

EUKARYOTA;

ANIMALS; CHROMATIN; CRYSTALLOGRAPHY, X-RAY; DNA; HISTONES; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NUCLEIC ACID CONFORMATION; NUCLEOSOMES; XENOPUS LAEVIS;

EID: 21844436803     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature03686     Document Type: Article

References (30)

1. Davey, C. A., Sargent, D. F., Luger, K., Maeder, A. W. & Richmond, T. J. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J. Mol. Biol. 319, 1097-1113 (2002).
2. Finch, J. T. & Klug, A. Solenoidal model for superstructure in chromatin. Proc. Natl Acad. Sci. USA 73, 1897-1901 (1976).
3. Williams, S. P. et al. Chromatin fibers are left-handed double helices with diameter and mass per unit length that depend on linker length. Biophys. J. 49, 233-248 (1986).
4. Richmond, T. J. & Davey, C. A. The structure of DNA in the nucleosome core. Nature 423, 145-150 (2003).
5. Oudet, P., Gross-Bellard, M. & Chambon, P. Electron microscopic and biochemical evidence that chromatin structure is a repeating unit. Cell 4, 281-300 (1975).
6. Thoma, F. & Koller, T. Influence of histone H1 on chromatin structure. Cell 12, 101-107 (1977).
7. Ris, H. & Korenberg, J. in Cell Biology (eds Prescott, D. M. & Goldstein, L.) 268-361 (Academic, New York, 1979).
8. Woodcock, C. L., Frado, L. L. & Rattner, J. B. The higher-order structure of chromatin: evidence for a helical ribbon arrangement. J. Cell Biol. 99, 42-52 (1984).
9. Widom, J., Finch, J. T. & Thomas, J. O. Higher-order structure of long repeat chromatin. EMBO J. 4, 3189-3194 (1985).
10. Woodcock, C. L. Chromatin fibers observed in situ in frozen hydrated sections. Native fiber diameter is not correlated with nucleosome repeat length. J. Cell Biol. 125, 11-19 (1994).
11. Butler, P. J. & Thomas, J. O. Changes in chromatin folding in solution. J. Mol. Biol. 140, 505-529 (1980).
12. McGhee, J. D., Nickol, J. M., Felsenfeld, G. & Rau, D. C. 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 (1983).
13. Athey, B. D., Smith, M. F., Rankert, D. A., Williams, S. P. & Langmore, J. P. The diameters of frozen-hydrated chromatin fibers increase with DNA linker length: evidence in support of variable diameter models for chromatin. J. Cell Biol. 111, 795-806 (1990).
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, 1-10 (1994).
15. Pehrson, J. R. Thymine dimer formation as a probe of the path of DNA in and between nucleosomes in intact chromatin. Proc. Natl Acad. Sci. USA 86, 9149-9153 (1989).
16. Dorigo, B., Schalch, T., Bystricky, K. & Richmond, T. J. Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J. Mol. Biol. 327, 85-96 (2003).
17. Dorigo, B. et al. Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science 306, 1571-1573 (2004).
18. Thomas, J. O. & Furber, V. Yeast chromatin structure. FEBS Lett. 66, 274-280 (1976).
19. Allan, J., Rau, D. C., Harborne, N. & Gould, H. Higher order structure in a short repeat length chromatin. J. Cell Biol. 98, 1320-1327 (1984).
20. Luger, K., Rechsteiner, T. J., Flaus, A. J., Waye, M. M. & Richmond, T. J. Characterization of nucleosome core particles containing histone proteins made in bacteria. J. Mol. Biol. 272, 301-311 (1997).
21. Gerchman, S. E. & Ramakrishnan, V. Chromatin higher-order structure studied by neutron scattering and scanning transmission electron microscopy. Proc. Natl Acad. Sci. USA 84, 7802-7806 (1987).
22. Sen, D., Mitra, S. & Crothers, D. M. Higher order structure of chromatin: evidence from photochemically detected linear dichroism. Biochemistry 25, 3441-3447 (1986).
23. Widom, J. & Klug, A. Structure of the 300 Å chromatin filament: X-ray diffraction from oriented samples. Cell 43, 207-213 (1985).
24. Graziano, V., Gerchman, S. E., Schneider, D. K. & Ramakrishnan, V. Histone H1 is located in the interior of the chromatin 30-nm filament. Nature 368, 351-354 (1994).
25. Blank, T. A. & Becker, P. B. Electrostatic mechanism of nucleosome spacing. J. Mol. Biol. 252, 305-313 (1995).
26. Korber, P. & Horz, W. In vitro assembly of the characteristic chromatin organization at the yeast PH05 promoter by a replication-independent extract system. J. Biol. Chem. 279, 35113-35120 (2004).
27. Read, R. Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr. D 57, 1373-1382 (2001).
28. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240-255 (1997).
29. Brünger, A. T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).
30. Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119 (1991).