title: 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.
abstract: 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.
authors.affiliation: Biozentrum and Swiss Institute of Bioinformatics, CH-4056 Basel, Switzerland.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Schlecht
authors.forename: Ionas
authors.initials: I
authors.lastname: Erb
authors.forename: Philippe
authors.initials: P
authors.lastname: Demougin
authors.forename: Nicolas
authors.initials: N
authors.lastname: Robine
authors.forename: Valérie
authors.initials: V
authors.lastname: Borde
authors.forename: Erik
authors.initials: E
authors.lastname: van Nimwegen
authors.forename: Alain
authors.initials: A
authors.lastname: Nicolas
authors.forename: Michael
authors.initials: M
authors.lastname: Primig
mesh_terms: D001665:Binding Sites; D019295:Computational Biology; D048749:Cytokinesis; D004271:DNA, Fungal / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D005285:Fermentation / Q000235:genetics*; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal / Q000235:genetics; D008540:Meiosis; D008938:Mitosis; D009154:Mutation / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D012689:Sequence Homology, Nucleic Acid; D013172:Spores, Fungal / Q000235:genetics* / Q000502:physiology; D013696:Temperature; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: C061886:ABF1 protein, S cerevisiae; D004271:DNA, Fungal; D004268:DNA-Binding Proteins; C065681:REB1 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors