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Molecular and Cellular Biology, November 2006, p. 8607-8622, Vol. 26, No. 22
0270-7306/06/$08.00+0     doi:10.1128/MCB.00678-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Activation of Saccharomyces cerevisiae HIS3 Results in Gcn4p-Dependent, SWI/SNF-Dependent Mobilization of Nucleosomes over the Entire Gene{triangledown}

Yeonjung Kim,1,{dagger} Neil McLaughlin,1 Kim Lindstrom,2 Toshio Tsukiyama,2 and David J. Clark1*

Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Building 6A, Room 2A14, 6 Center Drive, Bethesda, Maryland 20892,1 Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 981092

Received 19 April 2006/ Returned for modification 30 May 2006/ Accepted 3 September 2006

The effects of transcriptional activation on the chromatin structure of the Saccharomyces cerevisiae HIS3 gene were addressed by mapping the precise positions of nucleosomes in uninduced and induced chromatin. In the absence of the Gcn4p activator, the HIS3 gene is organized into a predominant nucleosomal array. In wild-type chromatin, this array is disrupted, and several alternative overlapping nucleosomal arrays are formed. The disruption of the predominant array also requires the SWI/SNF remodeling machine, indicating that the SWI/SNF complex plays an important role in nucleosome mobilization over the entire HIS3 gene. The Isw1 remodeling complex plays a more subtle role in determining nucleosome positions on HIS3, favoring positions different from those preferred by the SWI/SNF complex. Both the SWI/SNF and Isw1 complexes are constitutively present in HIS3 chromatin, although Isw1 tends to be excluded from the HIS3 promoter. Despite the apparent disorder of HIS3 chromatin generated by the formation of multiple nucleosomal arrays, nucleosome density profiles indicate that some long-range order is always present. We propose that Gcn4p stimulates nucleosome mobilization over the entire HIS3 gene by the SWI/SNF complex. We suggest that the net effect of interplay among remodeling machines at HIS3 is to create a highly dynamic chromatin structure.

* Corresponding author. Mailing address: Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Building 6A, Room 2A14, 6 Center Drive, Bethesda, MD 20892. Phone: (301) 496-6966. Fax: (301) 480-1907. E-mail: clarkda{at}mail.nih.gov.

{triangledown} Published ahead of print on 18 September 2006.

{dagger} Present address: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, KCDC, Seoul, South Korea.

Molecular and Cellular Biology, November 2006, p. 8607-8622, Vol. 26, No. 22
0270-7306/06/$08.00+0     doi:10.1128/MCB.00678-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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