Nucleosomes in solution exist as a mixture of twist-defect states - PubMed

Nucleosomes in solution exist as a mixture of twist-defect states

Rajeswari S Edayathumangalam et al. J Mol Biol. 2005.

Abstract

The 2.0 A crystal structure of a nucleosome core particle in complex with a bivalent pyrrole-imidazole polyamide reveals that this "clamp" effectively crossbraces the two gyres of the DNA superhelix, thereby stabilizing the nucleosome against dissociation. Using X-ray crystallography and footprinting techniques, we show that the clamp preferentially binds nucleosomes over free DNA, and that nucleosomal DNA exists as a mixture of multiple twist-defect intermediates in solution. The nucleosomes exist in one of two different conformations in various crystal structures that trap twist-defect intermediates, even on a strong positioning sequence. Evidence has been obtained supporting the existence of twist-defect states in nucleosomal DNA in solution that are similar to those obtained in crystal structures. Our results also substantiate the idea that twist diffusion may represent an important means of altering the accessibility of nucleosomal DNA both in the presence and in the absence of ATP-dependent chromatin-remodelling enzymes.

Similar articles

• Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands.

  Suto RK, Edayathumangalam RS, White CL, Melander C, Gottesfeld JM, Dervan PB, Luger K. Suto RK, et al. J Mol Biol. 2003 Feb 14;326(2):371-80. doi: 10.1016/s0022-2836(02)01407-9. J Mol Biol. 2003. PMID: 12559907

• Sequence-specific recognition of DNA in the nucleosome by pyrrole-imidazole polyamides.

  Gottesfeld JM, Melander C, Suto RK, Raviol H, Luger K, Dervan PB. Gottesfeld JM, et al. J Mol Biol. 2001 Jun 8;309(3):615-29. doi: 10.1006/jmbi.2001.4694. J Mol Biol. 2001. PMID: 11397084

• Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle.

  Tsunaka Y, Kajimura N, Tate S, Morikawa K. Tsunaka Y, et al. Nucleic Acids Res. 2005 Jun 10;33(10):3424-34. doi: 10.1093/nar/gki663. Print 2005. Nucleic Acids Res. 2005. PMID: 15951514 Free PMC article.

• Models for chromatin remodeling: a critical comparison.

  van Holde K, Yager T. van Holde K, et al. Biochem Cell Biol. 2003 Jun;81(3):169-72. doi: 10.1139/o03-038. Biochem Cell Biol. 2003. PMID: 12897850 Review.

• Chromatin: the nucleosome unwrapped.

  Widom J. Widom J. Curr Biol. 1997 Oct 1;7(10):R653-5. doi: 10.1016/s0960-9822(06)00327-7. Curr Biol. 1997. PMID: 9368751 Review.

Cited by

• Structure of RCC1 chromatin factor bound to the nucleosome core particle.

  Makde RD, England JR, Yennawar HP, Tan S. Makde RD, et al. Nature. 2010 Sep 30;467(7315):562-6. doi: 10.1038/nature09321. Epub 2010 Aug 25. Nature. 2010. PMID: 20739938 Free PMC article.

• A brief review of nucleosome structure.

  Cutter AR, Hayes JJ. Cutter AR, et al. FEBS Lett. 2015 Oct 7;589(20 Pt A):2914-22. doi: 10.1016/j.febslet.2015.05.016. Epub 2015 May 14. FEBS Lett. 2015. PMID: 25980611 Free PMC article. Review.

• Domain architecture of the catalytic subunit in the ISW2-nucleosome complex.

  Dang W, Bartholomew B. Dang W, et al. Mol Cell Biol. 2007 Dec;27(23):8306-17. doi: 10.1128/MCB.01351-07. Epub 2007 Oct 1. Mol Cell Biol. 2007. PMID: 17908792 Free PMC article.

• DNA stretching in the nucleosome facilitates alkylation by an intercalating antitumour agent.

  Davey GE, Wu B, Dong Y, Surana U, Davey CA. Davey GE, et al. Nucleic Acids Res. 2010 Apr;38(6):2081-8. doi: 10.1093/nar/gkp1174. Epub 2009 Dec 21. Nucleic Acids Res. 2010. PMID: 20026584 Free PMC article.

• Nucleosome structural studies.

  Tan S, Davey CA. Tan S, et al. Curr Opin Struct Biol. 2011 Feb;21(1):128-36. doi: 10.1016/j.sbi.2010.11.006. Epub 2010 Dec 19. Curr Opin Struct Biol. 2011. PMID: 21176878 Free PMC article. Review.

Publication types

MeSH terms

Substances