Protein & Cell

, Volume 1, Issue 11, pp 967–971 | Cite as

Dynamics of the higher-order structure of chromatin

Perspective

Abstract

Eukaryotic DNA is hierarchically packaged into chromatin to fit inside the nucleus. Dynamics of the chromatin structure plays a critical role in transcriptional regulation and other biological processes that involve DNA, such as DNA replication and DNA repair. Many factors, including histone variants, histone modification, DNA methylation and the binding of non-histone architectural proteins regulate the structure of chromatin. Although the structure of nucleosomes, the fundamental repeating unit of chromatin, is clear, there is still much discussion on the higher-order levels of chromatin structure. Identifying the structural details and dynamics of higher-order chromatin fibers is therefore very important for understanding the organization and regulation of gene activities. Here, we review studies on the dynamics of chromatin higherorder structure and its relationship with gene transcription.

Keywords

chromatin higher-order structure dynamics transcriptional regulation 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Angelov, D., Verdel, A., An, W., Bondarenko, V., Hans, F., Doyen, C. M., Studitsky, V.M., Hamiche, A., Roeder, R.G., Bouvet, P., et al. (2004). SWI/SNF remodeling and p300-dependent transcription of histone variant H2ABbd nucleosomal arrays. EMBO J 23, 3815–3824.CrossRefGoogle Scholar
  2. Bannister, A.J., Zegerman, P., Partridge, J.F., Miska, E.A., Thomas, J. O., Allshire, R.C., and Kouzarides, T. (2001). Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120–124.CrossRefGoogle Scholar
  3. Bussiek, M., Tóth, K., Schwarz, N., and Langowski, J. (2006). Trinucleosome compaction studied by fluorescence energy transfer and scanning force microscopy. Biochemistry 45, 10838–10846.CrossRefGoogle Scholar
  4. Catez, F., Ueda, T., and Bustin, M. (2006). Determinants of histone H1 mobility and chromatin binding in living cells. Nat Struct Mol Biol 13, 305–310.CrossRefGoogle Scholar
  5. Dorigo, B., Schalch, T., Kulangara, A., Duda, S., Schroeder, R.R., and Richmond, T.J. (2004). Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science 306, 1571–1573.CrossRefGoogle Scholar
  6. Eltsov, M., Maclellan, K.M., Maeshima, K., Frangakis, A.S., and Dubochet, J. (2008). Analysis of cryo-electron microscopy images does not support the existence of 30-nm chromatin fibers in mitotic chromosomes in situ. Proc Natl Acad Sci U S A 105, 19732–19737.CrossRefGoogle Scholar
  7. Fan, J.Y., Rangasamy, D., Luger, K., and Tremethick, D.J. (2004). H2A.Z alters the nucleosome surface to promote HP1alphamediated chromatin fiber folding. Mol Cell 16, 655–666.CrossRefGoogle Scholar
  8. Francis, N.J., Kingston, R.E., and Woodcock, C.L. (2004). Chromatin compaction by a polycomb group protein complex. Science 306, 1574–1577.CrossRefGoogle Scholar
  9. Gansen, A., Valeri, A., Hauger, F., Felekyan, S., Kalinin, S., Tóth, K., Langowski, J., and Seidel, C.A. (2009). Nucleosome disassembly intermediates characterized by single-molecule FRET. Proc Natl Acad Sci U S A 106, 15308–15313.CrossRefGoogle Scholar
  10. Hendzel, M.J., Lever, M.A., Crawford, E., and Th’ng, J.P. (2004). The C-terminal domain is the primary determinant of histone H1 binding to chromatin in vivo. J Biol Chem 279, 20028–20034.CrossRefGoogle Scholar
  11. Koopmans, W.J., Brehm, A., Logie, C., Schmidt, T., and van Noort, J. (2007). Single-pair FRET microscopy reveals mononucleosome dynamics. J Fluoresc 17, 785–795.CrossRefGoogle Scholar
  12. Li, G., Margueron, R., Hu, G., Stokes, D., Wang, Y.H., and Reinberg, D. (2010). Highly compacted chromatin formed in vitro reflects the dynamics of transcription activation in vivo. Mol Cell 38, 41–53.CrossRefGoogle Scholar
  13. Llères, D., James, J., Swift, S., Norman, D.G., and Lamond, A.I. (2009). Quantitative analysis of chromatin compaction in living cells using FLIM-FRET. J Cell Biol 187, 481–496.CrossRefGoogle Scholar
  14. 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 A resolution. Nature 389, 251–260.CrossRefGoogle Scholar
  15. Neumann, H., Hancock, S.M., Buning, R., Routh, A., Chapman, L., Somers, J., Owen-Hughes, T., van Noort, J., Rhodes, D., and Chin, J.W. (2009). A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation. Mol Cell 36, 153–163.CrossRefGoogle Scholar
  16. Poirier, M.G., Oh, E., Tims, H.S., and Widom, J. (2009). Dynamics and function of compact nucleosome arrays. Nat Struct Mol Biol 16, 938–944.CrossRefGoogle Scholar
  17. Robinson, P.J., Fairall, L., Huynh, V.A., and Rhodes, D. (2006). EM measurements define the dimensions of the “30-nm” chromatin fiber: evidence for a compact, interdigitated structure. Proc Natl Acad Sci U S A 103, 6506–6511.CrossRefGoogle Scholar
  18. Robinson, P.J., and Rhodes, D. (2006). Structure of the ‘30 nm’ chromatin fibre: a key role for the linker histone. Curr Opin Struct Biol 16, 336–343.CrossRefGoogle Scholar
  19. Routh, A., Sandin, S., and Rhodes, D. (2008). Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure. Proc Natl Acad Sci U S A 105, 8872–8877.CrossRefGoogle Scholar
  20. Schalch, T., Duda, S., Sargent, D.F., and Richmond, T.J. (2005). X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature 436, 138–141.CrossRefGoogle Scholar
  21. Shogren-Knaak, M., Ishii, H., Sun, J.M., Pazin, M.J., Davie, J.R., and Peterson, C.L. (2006). Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311, 844–847.CrossRefGoogle Scholar
  22. Strick, R., Strissel, P.L., Gavrilov, K., and Levi-Setti, R. (2001). Cationchromatin binding as shown by ion microscopy is essential for the structural integrity of chromosomes. J Cell Biol 155, 899–910.CrossRefGoogle Scholar
  23. Thoma, F., Koller, T., 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.CrossRefGoogle Scholar
  24. Trojer, P., Li, G., Sims, R.J. 3rd, Vaquero, A., Kalakonda, N., Boccuni, P., Lee, D., Erdjument-Bromage, H., Tempst, P., Nimer, S.D., et al. (2007). L3MBTL1, a histone-methylation-dependent chromatin lock. Cell 129, 915–928.CrossRefGoogle Scholar
  25. Watanabe, S., Resch, M., Lilyestrom, W., Clark, N., Hansen, J.C., Peterson, C., and Luger, K. (2010). Structural characterization of H3K56Q nucleosomes and nucleosomal arrays. Biochim Biophys Acta 1799, 480–486.CrossRefGoogle Scholar
  26. Widom, J., and Klug, A. (1985). Structure of the 300A chromatin filament: X-ray diffraction from oriented samples. Cell 43, 207–213.CrossRefGoogle Scholar
  27. 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.CrossRefGoogle Scholar
  28. Woodcock, C.L., Frado, L.L., and Rattner, J.B. (1984). The higherorder structure of chromatin: evidence for a helical ribbon arrangement. J Cell Biol 99, 42–52.CrossRefGoogle Scholar
  29. Zlatanova, J., Caiafa, P., and Van Holde, K. (2000). Linker histone binding and displacement: versatile mechanism for transcriptional regulation. FASEB J 14, 1697–1704.CrossRefGoogle Scholar

Copyright information

© Higher Education Press and Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  1. 1.Institute of BiophysicsChinese Academy of SciencesBeijingChina

Personalised recommendations