A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters

• DOI: 10.1016/j.molcel.2008.11.020
• Publication Date: 2008-12-25T10:32:05Z
• Authors: Gwenael Badis; Esther T. Chan; Harm van Bakel; Lourdes Pena-Cast...; Desiree Tillo; Kyle Tsui; Clayton D. Carlson; Andrea J. Gossett; Michael J. Hasinoff; Christopher L. Wa...; Marinella Gebbia; Shaheynoor Talukder; Ally Yang; Sanie Mnaimneh; Dimitri Terterov; David Coburn; Ai Li Yeo; Zhen Xuan Yeo; Neil D. Clarke; Jason D. Lieb; Aseem Z. Ansari; Corey Nislow; Timothy R. Hughes
• Keywords: 0301 basic medicine; 0303 health sciences; Binding Sites; Saccharomyces cerevisiae Proteins; Base Sequence; Sequence Homology, Amino Acid; [SDV]Life Sciences [q-bio]; Genes, Fungal; Molecular Sequence Data; Reproducibility of Results; Cell Biology; Saccharomyces cerevisiae; Nucleosomes; DNA-Binding Proteins; 03 medical and health sciences; Mutation; Promoter Regions, Genetic; Molecular Biology; Phylogeny; Transcription Factors

The sequence specificity of DNA-binding proteins is the primary mechanism by which the cell recognizes genomic features. Here, we describe systematic determination of yeast transcription factor DNA-binding specificities. We obtained binding specificities for 112 DNA-binding proteins representing 19 distinct structural classes, one-third of which have not been previously reported. Several newly discovered binding sequences have striking genomic distributions relative to transcription start sites, supporting their biological relevance and suggesting a role in promoter architecture. Among these are Rsc3 binding sequences, containing the core CGCG, which are found preferentially ~100 bp upstream of transcription start sites. Mutation of RSC3 results in a dramatic increase in nucleosome occupancy in hundreds of proximal promoters containing a Rsc3 binding element, but has little impact on promoters lacking Rsc3 binding sequences, indicating that Rsc3 plays a broad role in targeting nucleosome exclusion at yeast promoters.