title: A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.
abstract: 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 the binding specificities have not been previously reported. Several 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 approximately 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.
authors.affiliation: Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
authors.forename: Gwenael
authors.initials: G
authors.lastname: Badis
authors.forename: Esther T
authors.initials: ET
authors.lastname: Chan
authors.forename: Harm
authors.initials: H
authors.lastname: van Bakel
authors.forename: Lourdes
authors.initials: L
authors.lastname: Pena-Castillo
authors.forename: Desiree
authors.initials: D
authors.lastname: Tillo
authors.forename: Kyle
authors.initials: K
authors.lastname: Tsui
authors.forename: Clayton D
authors.initials: CD
authors.lastname: Carlson
authors.forename: Andrea J
authors.initials: AJ
authors.lastname: Gossett
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Hasinoff
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Warren
authors.forename: Marinella
authors.initials: M
authors.lastname: Gebbia
authors.forename: Shaheynoor
authors.initials: S
authors.lastname: Talukder
authors.forename: Ally
authors.initials: A
authors.lastname: Yang
authors.forename: Sanie
authors.initials: S
authors.lastname: Mnaimneh
authors.forename: Dimitri
authors.initials: D
authors.lastname: Terterov
authors.forename: David
authors.initials: D
authors.lastname: Coburn
authors.forename: Ai
authors.initials: A
authors.lastname: Li Yeo
authors.forename: Zhen Xuan
authors.initials: ZX
authors.lastname: Yeo
authors.forename: Neil D
authors.initials: ND
authors.lastname: Clarke
authors.forename: Jason D
authors.initials: JD
authors.lastname: Lieb
authors.forename: Aseem Z
authors.initials: AZ
authors.lastname: Ansari
authors.forename: Corey
authors.initials: C
authors.lastname: Nislow
authors.forename: Timothy R
authors.initials: TR
authors.lastname: Hughes
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000378:metabolism*; D005800:Genes, Fungal; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D009707:Nucleosomes / Q000378:metabolism*; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D009707:Nucleosomes; C103337:RSC complex, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors