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Vol. 19, Issue 5, 2193-2207, May 2008

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Genome-wide Expression Profiling, In Vivo DNA Binding Analysis, and Probabilistic Motif Prediction Reveal Novel Abf1 Target Genes during Fermentation, Respiration, and Sporulation in Yeast

Ulrich Schlecht^*,, Ionas Erb^*, Philippe Demougin^*, Nicolas Robine^,, Valérie Borde, Erik van Nimwegen^*, Alain Nicolas, and Michael Primig^*,||

*Biozentrum and Swiss Institute of Bioinformatics, CH-4056 Basel, Switzerland; Centre National de la Recherche Scientifique Unité Mixte de Recherche 7147 Recombination and Genome Instability, Institut Curie, Université Pierre et Marie Curie, F-75248 Paris, France; and Service de Bioinformatique, Institut Curie, F-75248 Paris, France

Submitted December 19, 2007; Revised February 14, 2008; Accepted February 19, 2008
Monitoring Editor: Mark Solomon

The autonomously replicating sequence binding factor 1 (Abf1) was initially identified as an essential DNA replication factor and later shown to be a component of the regulatory network controlling mitotic and meiotic cell cycle progression in budding yeast. The protein is thought to exert its functions via specific interaction with its target site as part of distinct protein complexes, but its roles during mitotic growth and meiotic development are only partially understood. Here, we report a comprehensive approach aiming at the identification of direct Abf1-target genes expressed during fermentation, respiration, and sporulation. Computational prediction of the protein's target sites was integrated with a genome-wide DNA binding assay in growing and sporulating cells. The resulting data were combined with the output of expression profiling studies using wild-type versus temperature-sensitive alleles. This work identified 434 protein-coding loci as being transcriptionally dependent on Abf1. More than 60% of their putative promoter regions contained a computationally predicted Abf1 binding site and/or were bound by Abf1 in vivo, identifying them as direct targets. The present study revealed numerous loci previously unknown to be under Abf1 control, and it yielded evidence for the protein's variable DNA binding pattern during mitotic growth and meiotic development.

Author contributions: U.S. designed and performed research and analyzed data. I.E. and E.v.N. provided binding site predictions and analyzed data. P.D. produced the microarray data. N.R. and V.B. supported ChIP-Chip data production and provided analysis procedures. A.N. designed research. M.P. designed research, interpreted data, and wrote the paper.

Present addresses: Stanford Genome Technology Center, 855 California Ave., Palo Alto, CA 94304;

^|| Institut National de la Santé et de la Recherche Médicale Unité 625, Université de Rennes 1, F-35042 Rennes, France.

Address correspondence to: Michael Primig (michael.primig{at}rennes.inserm.fr)