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J. Biol. Chem., Vol. 279, Issue 33, 34865-34872, August 13, 2004

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Genome-wide Analysis of ARS (Autonomously Replicating Sequence) Binding Factor 1 (Abf1p)-mediated Transcriptional Regulation in Saccharomyces cerevisiae^*

Tsuyoshi Miyake, Justin Reese, Christian M. Loch, David T. Auble, and Rong Li

From the Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, Virginia 22908-0733

Autonomously replicating sequence-binding factor-1 (Abf1p) is an essential sequence-specific transcription factor in Saccharomyces cerevisiae that participates in multiple nuclear events including DNA replication, transcription activation, and gene silencing. Numerous gene-specific analyses have implicated Abf1p in the transcriptional control of genes involved in a diverse range of cellular functions, leading to the notion that Abf1p acts as a global transcriptional regulator. Here we report findings from a genome-wide comparison of the gene expression profiles in the wild-type and abf1-1 temperature-sensitive mutant. The study identifies a total of 86 Abf1p-regulated genes (1.4% of the genome) of which 50 are activated and 36 are repressed by Abf1p. Interestingly, Abf1p binds to its own promoter in vivo and strongly represses its own transcription, suggesting a potential negative regulatory loop in Abf1p-mediated gene regulation. A comparison of our microarray data with the available databases reveals a significant overlap of genes regulated by Abf1p and those by several general transcription factors such as Mot1p and TAFs (TATA-binding protein-associated factors). Different mutant alleles of abf1 affect Abf1p-mediated transcription in a gene-dependent manner. Furthermore, Abf1p in vivo is associated with the promoter region of most Abf1p-activated but not with that of most Abf1p-repressed genes. Taken together, these results strongly suggest distinct underlying mechanisms by which Abf1p regulates gene expression.

Received for publication, May 10, 2004 , and in revised form, June 4, 2004.

The amino acid sequence of this protein can be accessed through NCBI Protein Database under NCBI accession numbers GSM25879, GSM25880, GSM25881, GSM25882, and GSE1492.

^* The work was supported by National Institutes of Health Grants GM57893 (to R. L.) and GM55763 (to D. T. A.). 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 Supplemental Tables 1, A and B.

To whom correspondence should be addressed: Dept. of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, P. O. Box 800733, Charlottesville, VA 22908-0733. Tel.: 434-243-2727; Fax: 434-924-5069; E-mail: rl2t{at}virginia.edu.

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