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PMID: 19111667 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.

Molecular cell ·Vol. 32 ·No. 6 ·2008-12-26 ·Pages 878-87

Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR

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.

MeSH Terms
Base Sequence Binding Sites DNA-Binding Proteins/metabolism Genes, Fungal Molecular Sequence Data Mutation/genetics Nucleosomes/metabolism Phylogeny Promoter Regions, Genetic Reproducibility of Results Saccharomyces cerevisiae/genetics Saccharomyces cerevisiae Proteins/metabolism Sequence Homology, Amino Acid Transcription Factors/genetics,metabolism
Chemicals
DNA-Binding Proteins Nucleosomes RSC complex, S cerevisiae Saccharomyces cerevisiae Proteins Transcription Factors
Authors & Affiliations
23 authors, click to expand affiliations / ORCID
Badis Gwenael
Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
Chan Esther T
van Bakel Harm
Pena-Castillo Lourdes
Tillo Desiree
Tsui Kyle
Carlson Clayton D
Gossett Andrea J
Hasinoff Michael J
Warren Christopher L
Gebbia Marinella
Talukder Shaheynoor
Yang Ally
Mnaimneh Sanie
Terterov Dimitri
Coburn David
Li Yeo Ai
Yeo Zhen Xuan
Clarke Neil D
Lieb Jason D
Ansari Aseem Z
Nislow Corey
Hughes Timothy R
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Article Info
Journal
Molecular cell
Abbr.
Mol Cell
ISSN
1097-4164
DOI
10.1016/j.molcel.2008.11.020
Published
2008-12-26
Pages
878-87
Language
English
Region
United States
NLM ID
9802571
PMCID
PMC2743730
Subset
IM
Grants
NIGMS NIH HHS · R01-GM072518 · United States
NLM NIH HHS · T15LM007359 · United States
NIGMS NIH HHS · R01 GM072518-02 · United States
NLM NIH HHS · T15 LM007359 · United States
NIGMS NIH HHS · R01 GM072518-03 · United States
NIGMS NIH HHS · R01 GM069420-04 · United States
NIGMS NIH HHS · R01 GM069420 · United States
NIGMS NIH HHS · R01 GM072518 · United States
NIGMS NIH HHS · R01 GM072518-01A1 · United States
Databases
GEO
GSE12349
External Links
PubMed source DOI: 10.1016/j.molcel.2008.11.020 PMC Full Text View journal details
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