Schlecht U, et al. (2008) 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. Mol Biol Cell 19(5):2193-2207
Abstract: Monitoring Editor: Mark Solomon The DNA-binding 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 yielded evidence for the protein's variable DNA binding pattern during mitotic growth and meiotic development.
|Status: Published||Type: Journal Article||PubMed ID: 18305101|
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|Genomic expression study|
|Protein-Nucleic Acid Interactions|