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

Article metrics

Abstract

DNA in eukaryotic chromosomes is organized in arrays of nucleosomes compacted into chromatin fibres. This higher-order structure of nucleosomes is the substrate for DNA replication, recombination, transcription and repair. Although the structure of the nucleosome core is known at near-atomic resolution1, even the most fundamental information about the organization of nucleosomes in the fibre is controversial. Here we report the crystal structure of an oligonucleosome (a compact tetranucleosome) at 9 Å resolution, solved by molecular replacement using the nucleosome core structure. The structure shows that linker DNA zigzags back and forth between two stacks of nucleosome cores, which form a truncated two-start helix, and does not follow a path compatible with a one-start solenoidal helix2. The length of linker DNA is most probably buffered by stretching of the DNA contained in the nucleosome cores. We have built continuous fibre models by successively stacking tetranucleosomes one on another. The resulting models are nearly fully compacted and most closely resemble the previously described crossed-linker model3. They suggest that the interfaces between nucleosomes along a single helix start are polymorphic.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Tetranucleosome structure.
Figure 2: Electron density for the linker DNA (stereographs).
Figure 3: Chromatin fibre models.

References

  1. 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. 2

    Finch, J. T. & Klug, A. Solenoidal model for superstructure in chromatin. Proc. Natl Acad. Sci. USA 73, 1897–1901 (1976)

  3. 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. 4

    Richmond, T. J. & Davey, C. A. The structure of DNA in the nucleosome core. Nature 423, 145–150 (2003)

  5. 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. 6

    Thoma, F. & Koller, T. Influence of histone H1 on chromatin structure. Cell 12, 101–107 (1977)

  7. 7

    Ris, H. & Korenberg, J. in Cell Biology (eds Prescott, D. M. & Goldstein, L.) 268–361 (Academic, New York, 1979)

  8. 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. 9

    Widom, J., Finch, J. T. & Thomas, J. O. Higher-order structure of long repeat chromatin. EMBO J. 4, 3189–3194 (1985)

  10. 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. 11

    Butler, P. J. & Thomas, J. O. Changes in chromatin folding in solution. J. Mol. Biol. 140, 505–529 (1980)

  12. 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. 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. 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. 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. 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. 17

    Dorigo, B. et al. Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science 306, 1571–1573 (2004)

  18. 18

    Thomas, J. O. & Furber, V. Yeast chromatin structure. FEBS Lett. 66, 274–280 (1976)

  19. 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. 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. 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. 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. 23

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

  24. 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. 25

    Blank, T. A. & Becker, P. B. Electrostatic mechanism of nucleosome spacing. J. Mol. Biol. 252, 305–313 (1995)

  26. 26

    Korber, P. & Horz, W. In vitro assembly of the characteristic chromatin organization at the yeast PHO5 promoter by a replication-independent extract system. J. Biol. Chem. 279, 35113–35120 (2004)

  27. 27

    Read, R. Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr. D 57, 1373–1382 (2001)

  28. 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. 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. 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)

Download references

Acknowledgements

We thank C. Schulze-Briese, T. Tomizaki and A. Wagner for assistance in data collection, and J. Widom for providing us with the 601 sequence.

Author information

Correspondence to Timothy J. Richmond.

Ethics declarations

Competing interests

Coordinates have been deposited in the Protein Data Bank with identifier 1zbb. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Supplementary information

Supplementary Figure S1

Explanation of the packing disorder found in the tetranucleosome crystals. (PDF 96 kb)

Supplementary Figure S2

Small angle X-ray scattering (SAXS) distributions for chicken erythrocyte chromatin and three chromatin fibre models. (PDF 54 kb)

Supplementary Methods

Description of the sequence and preparation of the DNA contained in the tetranucleosome. (PDF 11 kb)

Supplementary Table S1

Statistics of the X-ray crystallographic structure determination. (PDF 50 kb)

Supplementary Video S1

Tetranucleosome with axis system displayed (video version of Fig. 1c). (WMV 7692 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Schalch, T., Duda, S., Sargent, D. et al. X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature 436, 138–141 (2005) doi:10.1038/nature03686

Download citation

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.