A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.
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.
Badis
Gwenael
G
Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
Chan
Esther T
ET
van Bakel
Harm
H
Pena-Castillo
Lourdes
L
Tillo
Desiree
D
Tsui
Kyle
K
Carlson
Clayton D
CD
Gossett
Andrea J
AJ
Hasinoff
Michael J
MJ
Warren
Christopher L
CL
Gebbia
Marinella
M
Talukder
Shaheynoor
S
Yang
Ally
A
Mnaimneh
Sanie
S
Terterov
Dimitri
D
Coburn
David
D
Li Yeo
Ai
A
Yeo
Zhen Xuan
ZX
Clarke
Neil D
ND
Lieb
Jason D
JD
Ansari
Aseem Z
AZ
Nislow
Corey
C
Hughes
Timothy R
TR
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
D004268:DNA-Binding Proteins; D009707:Nucleosomes; C103337:RSC complex, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors