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Molecular and Cellular Biology, March 2005, p. 2138-2146, Vol. 25, No. 6
0270-7306/05/$08.00+0     doi:10.1128/MCB.25.6.2138-2146.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Combined Global Localization Analysis and Transcriptome Data Identify Genes That Are Directly Coregulated by Adr1 and Cat8{dagger}

Christine Tachibana,1 Jane Y. Yoo,2 Jean-Basco Tagne,2 Nataly Kacherovsky,1 Tong I. Lee,2 and Elton T. Young1*

Department of Biochemistry, University of Washington, Seattle, Washington,1 Whitehead Institute for Biomedical Research, Cambridge, Massachusetts2

Received 26 August 2004/ Returned for modification 5 October 2004/ Accepted 20 December 2004

In Saccharomyces cerevisiae, glucose depletion causes a profound alteration in metabolism, mediated in part by global transcriptional changes. Many of the transcription factors that regulate these changes act combinatorially. We have analyzed combinatorial regulation by Adr1 and Cat8, two transcription factors that act during glucose depletion, by combining genome-wide expression and genome-wide binding data. We identified 32 genes that are directly activated by Adr1, 28 genes that are directly activated by Cat8, and 14 genes that are directly regulated by both. Our analysis also uncovered promoters that Adr1 binds but does not regulate and promoters that are indirectly regulated by Cat8, stressing the advantage of combining global expression and global localization analysis to find directly regulated targets. At most of the coregulated promoters, the in vivo binding of one factor is independent of the other, but Adr1 is required for optimal Cat8 binding at two promoters with a poor match to the Cat8 binding consensus. In addition, Cat8 is required for Adr1 binding at promoters where Adr1 is not required for transcription. These data provide a comprehensive analysis of the direct, indirect, and combinatorial requirements for these two global transcription factors.

* Corresponding author. Mailing address: Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195-7350. Phone: (206) 543-6517. Fax: (206) 685-1792. E-mail: ety{at}u.washington.edu.

{dagger} Supplemental material for this article may be found at http://mcb.asm.org/.

Molecular and Cellular Biology, March 2005, p. 2138-2146, Vol. 25, No. 6
0022-538X/05/$08.00+0     doi:10.1128/MCB.25.6.2138-2146.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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