This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Anderson, J. D.
Right arrow Articles by Widom, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Anderson, J. D.
Right arrow Articles by Widom, J.

 Previous Article  |  Next Article 

Molecular and Cellular Biology, October 2002, p. 7147-7157, Vol. 22, No. 20
0270-7306/02/$04.00+0     DOI: 10.1128/MCB.22.20.7147-7157.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Spontaneous Access of Proteins to Buried Nucleosomal DNA Target Sites Occurs via a Mechanism That Is Distinct from Nucleosome Translocation

J. D. Anderson, A. Thåström, and J. Widom*

Department of Biochemistry, Molecular Biology, and Cell Biology and Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3500

Received 28 May 2002/ Returned for modification 16 July 2002/ Accepted 23 July 2002

Intrinsic nucleosome dynamics termed "site exposure" provides spontaneous and cooperative access to buried regions of nucleosomal DNA in vitro. Two different mechanisms for site exposure have been proposed, one based on nucleosome translocation, the other on dynamic nucleosome conformational changes in which a stretch of the nucleosomal DNA is transiently released off the histone surface. Here we report on three experiments that distinguish between these mechanisms. One experiment investigates the effects on the accessibilities of restriction enzyme target sites inside nucleosomes when extra DNA (onto which the nucleosome may move at low energetic cost) is appended onto one end. The other two experiments test directly for nucleosome mobility under the conditions used to probe accessibility to restriction enzymes: one on a selected nonnatural nucleosome positioning sequence, the other on the well-studied 5S rRNA gene nucleosome positioning sequence. We find from all three assays that restriction enzymes gain access to sites throughout the entire length of the nucleosomal DNA without contribution from nucleosome translocation. We conclude that site exposure in nucleosomes in vitro occurs via a nucleosome conformational change that leads to transient release of a stretch of DNA from the histone surface, most likely involving progressive uncoiling from an end. Recapture at a distal site along DNA that has partially uncoiled would result in looped structures which are believed to contribute to RNA polymerase elongation and may contribute to spontaneous or ATP-driven nucleosome mobility. Transient open states may facilitate the initial entry of transcription factors and enzymes in vivo.

* Corresponding author. Mailing address: Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2153 Sheridan Rd., Evanston, IL 60208-3500. Phone: (847) 467-1887. Fax: (847) 467-1380. E-mail: j-widom{at}northwestern.edu.

Molecular and Cellular Biology, October 2002, p. 7147-7157, Vol. 22, No. 20
0022-538X/02/$04.00+0     DOI: 10.1128/MCB.22.20.7147-7157.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Gottschalk, A. J., Timinszky, G., Kong, S. E., Jin, J., Cai, Y., Swanson, S. K., Washburn, M. P., Florens, L., Ladurner, A. G., Conaway, J. W., Conaway, R. C. (2009). Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler. Proc. Natl. Acad. Sci. USA 106: 13770-13774 [Abstract] [Full Text]  
  • Sims, H. I., Baughman, C. B., Schnitzler, G. R. (2008). Human SWI/SNF directs sequence-specific chromatin changes on promoter polynucleosomes. Nucleic Acids Res 36: 6118-6131 [Abstract] [Full Text]  
  • Prasad, A., Wallace, S. S., Pederson, D. S. (2007). Initiation of Base Excision Repair of Oxidative Lesions in Nucleosomes by the Human, Bifunctional DNA Glycosylase NTH1. Mol. Cell. Biol. 27: 8442-8453 [Abstract] [Full Text]  
  • Yang, Z., Zheng, C., Hayes, J. J. (2007). The Core Histone Tail Domains Contribute to Sequence-dependent Nucleosome Positioning. J. Biol. Chem. 282: 7930-7938 [Abstract] [Full Text]  
  • Francis, J., Babu, D. A., Deering, T. G., Chakrabarti, S. K., Garmey, J. C., Evans-Molina, C., Taylor, D. G., Mirmira, R. G. (2006). Role of Chromatin Accessibility in the Occupancy and Transcription of the Insulin Gene by the Pancreatic and Duodenal Homeobox Factor 1. Mol. Endocrinol. 20: 3133-3145 [Abstract] [Full Text]  
  • Mersfelder, E. L., Parthun, M. R. (2006). The tale beyond the tail: histone core domain modifications and the regulation of chromatin structure.. Nucleic Acids Res 34: 2653-2662 [Abstract] [Full Text]  
  • Ulyanova, N. P., Schnitzler, G. R. (2005). Human SWI/SNF Generates Abundant, Structurally Altered Dinucleosomes on Polynucleosomal Templates. Mol. Cell. Biol. 25: 11156-11170 [Abstract] [Full Text]  
  • Okuwaki, M., Kato, K., Shimahara, H., Tate, S.-i., Nagata, K. (2005). Assembly and Disassembly of Nucleosome Core Particles Containing Histone Variants by Human Nucleosome Assembly Protein I. Mol. Cell. Biol. 25: 10639-10651 [Abstract] [Full Text]  
  • Yang, Z., Zheng, C., Thiriet, C., Hayes, J. J. (2005). The Core Histone N-Terminal Tail Domains Negatively Regulate Binding of Transcription Factor IIIA to a Nucleosome Containing a 5S RNA Gene via a Novel Mechanism. Mol. Cell. Biol. 25: 241-249 [Abstract] [Full Text]  
  • Wu, C., Travers, A. (2004). A 'one-pot' assay for the accessibility of DNA in a nucleosome core particle. Nucleic Acids Res 32: e122-e122 [Abstract] [Full Text]  
  • Case, R. B., Chang, Y.-P., Smith, S. B., Gore, J., Cozzarelli, N. R., Bustamante, C. (2004). The Bacterial Condensin MukBEF Compacts DNA into a Repetitive, Stable Structure. Science 305: 222-227 [Abstract] [Full Text]  
  • Belikov, S., Astrand, C., Holmqvist, P.-H., Wrange, O. (2004). Chromatin-Mediated Restriction of Nuclear Factor 1/CTF Binding in a Repressed and Hormone-Activated Promoter In Vivo. Mol. Cell. Biol. 24: 3036-3047 [Abstract] [Full Text]  
  • Okuwaki, M., Verreault, A. (2004). Maintenance DNA Methylation of Nucleosome Core Particles. J. Biol. Chem. 279: 2904-2912 [Abstract] [Full Text]  
  • Ragab, A., Travers, A. (2003). HMG-D and histone H1 alter the local accessibility of nucleosomal DNA. Nucleic Acids Res 31: 7083-7089 [Abstract] [Full Text]  
  • Beard, B. C., Wilson, S. H., Smerdon, M. J. (2003). Suppressed catalytic activity of base excision repair enzymes on rotationally positioned uracil in nucleosomes. Proc. Natl. Acad. Sci. USA 100: 7465-7470 [Abstract] [Full Text]  
  • Miller, J. A., Widom, J. (2003). Collaborative Competition Mechanism for Gene Activation In Vivo. Mol. Cell. Biol. 23: 1623-1632 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»