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Molecular and Cellular Biology, April 2007, p. 3217-3225, Vol. 27, No. 8
0270-7306/07/$08.00+0     doi:10.1128/MCB.01731-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Dependency of ISW1a Chromatin Remodeling on Extranucleosomal DNA{triangledown}

Vamsi K. Gangaraju{dagger} and Blaine Bartholomew*

Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901-4413

Received 13 September 2006/ Returned for modification 12 November 2006/ Accepted 18 January 2007

The nucleosome remodeling activity of ISW1a was dependent on whether ISW1a was bound to one or both extranucleosomal DNAs. ISW1a preferentially bound nucleosomes with an optimal length of ~33 to 35 bp of extranucleosomal DNA at both the entry and exit sites over nucleosomes with extranucleosomal DNA at only one entry or exit site. Nucleosomes with extranucleosomal DNA at one of the entry/exit sites were readily remodeled by ISW1a and stimulated the ATPase activity of ISW1a, while conversely, nucleosomes with extranucleosomal DNA at both entry/exit sites were unable either to stimulate the ATPase activity of ISW1a or to be mobilized. DNA footprinting revealed that a major conformational difference between the nucleosomes was the lack of ISW1a binding to nucleosomal DNA two helical turns from the dyad axis in nucleosomes with extranucleosomal DNA at both entry/exit sites. The Ioc3 subunit of ISW1a was found to be the predominant subunit associated with extranucleosomal DNA when ISW1a is bound either to one or to both extranucleosomal DNAs. These two conformations of the ISW1a-nucleosome complex are suggested to be the molecular basis for the nucleosome spacing activity of ISW1a on nucleosomal arrays. ISW1b, the other isoform of ISW1, does not have the same dependency for extranucleosomal DNA as ISW1a and, likewise, is not able to space nucleosomes.

* Corresponding author. Mailing address: Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, 1245 Lincoln Dr., Neckers Bldg. Room 229, Carbondale, IL 62901-4413. Phone: (618) 453-6437. Fax: (618) 453-6440. E-mail: bbartholomew{at}siumed.edu

{triangledown} Published ahead of print on 5 February 2007.

{dagger} Present address: Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, NS287, New Haven, CT 06520.

Molecular and Cellular Biology, April 2007, p. 3217-3225, Vol. 27, No. 8
0270-7306/07/$08.00+0     doi:10.1128/MCB.01731-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Teif, V. B., Rippe, K. (2009). Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities. Nucleic Acids Res 37: 5641-5655 [Abstract] [Full Text]  
  • Pinskaya, M., Nair, A., Clynes, D., Morillon, A., Mellor, J. (2009). Nucleosome Remodeling and Transcriptional Repression Are Distinct Functions of Isw1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 29: 2419-2430 [Abstract] [Full Text]  


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