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J. Biol. Chem., Vol. 281, Issue 37, 27346-27355, September 15, 2006

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Widespread, but Non-identical, Association of Proteasomal 19 and 20 S Proteins with Yeast Chromatin^*

Devanjan Sikder, Stephen Albert Johnston¹, and Thomas Kodadek²

From the Division of Translational Research, Department of Internal Medicine and Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8573

It has recently become clear that various aspects of nucleic acid metabolism and the ubiquitin-proteasome pathway intersect in several direct and important ways. To begin to assess the scope of some of these activities in the yeast Saccharomyces cerevisiae, we assessed the physical and functional association of proteasomal proteins from both the 20 S core and 19 S regulatory particles with 6400 yeast genes. Genome-wide chromatin immunoprecipitation analyses revealed that proteasome substituents are associated with the majority of yeast genes. Many of these associations correlated strongly with expression levels and the presence of RNA polymerase II. Although the data support the presence of the intact 26 S proteasome on most genes, several hundred yeast genes were cross-linked to either the 20 or 19 S complex but not both, consistent with some degree of independent function for the proteasomal subcomplexes.

Received for publication, May 17, 2006 , and in revised form, July 10, 2006.

^* This work was funded with federal funds as part of the NHLBI Proteomics Initiative of the NHLBI, National Institutes of Health, under Contract Number NO1-HV-28185 and by National Institutes of Health Grant GM066380. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supporting information.

¹ Present address: Center for Innovation in Medicine, Biodesign Inst., Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85287-5001.

² To whom correspondence should be addressed: Center for Biomedical Inventions and Depts. of Internal Medicine and Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-8573. E-mail: Thomas.Kodadek{at}utsouthwestern.edu.

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