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Molecular and Cellular Biology, June 2009, p. 2960-2981, Vol. 29, No. 11
0270-7306/09/$08.00+0     doi:10.1128/MCB.01054-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Differential Cofactor Requirements for Histone Eviction from Two Nucleosomes at the Yeast PHO84 Promoter Are Determined by Intrinsic Nucleosome Stability{triangledown}

Christian J. Wippo,1 Bojana Silic Krstulovic,2 Franziska Ertel,1 Sanja Musladin,2 Dorothea Blaschke,1 Sabrina Stürzl,1 Guo-Cheng Yuan,3 Wolfram Hörz,1,{dagger} Philipp Korber,1* and Slobodan Barbaric2

Adolf-Butenandt-Institut, Universität München, Munich, Germany,1 Laboratory of Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia,2 Department of Biostatistics, Harvard School of Public Health, and Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts3

Received 4 July 2008/ Returned for modification 6 August 2008/ Accepted 1 March 2009

We showed previously that the strong PHO5 promoter is less dependent on chromatin cofactors than the weaker coregulated PHO8 promoter. In this study we asked if chromatin remodeling at the even stronger PHO84 promoter was correspondingly less cofactor dependent. The repressed PHO84 promoter showed a short hypersensitive region that was flanked upstream and downstream by a positioned nucleosome and contained two transactivator Pho4 sites. Promoter induction generated an extensive hypersensitive and histone-depleted region, yielding two more Pho4 sites accessible. This remodeling was strictly Pho4 dependent, strongly dependent on the remodelers Snf2 and Ino80 and on the histone acetyltransferase Gcn5, and more weakly on the acetyltransferase Rtt109. Importantly, remodeling of each of the two positioned nucleosomes required Snf2 and Ino80 to different degrees. Only remodeling of the upstream nucleosome was strictly dependent on Snf2. Further, remodeling of the upstream nucleosome was more dependent on Ino80 than remodeling of the downstream nucleosome. Both nucleosomes differed in their intrinsic stabilities as predicted in silico and measured in vitro. The causal relationship between the different nucleosome stabilities and the different cofactor requirements was shown by introducing destabilizing mutations in vivo. Therefore, chromatin cofactor requirements were determined by intrinsic nucleosome stabilities rather than correlated to promoter strength.

* Corresponding author. Mailing address: Adolf-Butenandt-Institut, Universität München, Schillerstr. 44, 80336 Munich, Germany. Phone: 49-89-218075435. Fax: 49-89-218075425. E-mail: pkorber{at}lmu.de

{triangledown} Published ahead of print on 23 March 2009.

{dagger} Deceased, 13 November 2005.

Molecular and Cellular Biology, June 2009, p. 2960-2981, Vol. 29, No. 11
0270-7306/09/$08.00+0     doi:10.1128/MCB.01054-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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