title: Nonspecific protein-DNA binding is widespread in the yeast genome.
abstract: Recent genome-wide measurements of binding preferences of ~200 transcription regulators in the vicinity of transcription start sites in yeast, have provided a unique insight into the cis-regulatory code of a eukaryotic genome. Here, we show that nonspecific transcription factor (TF)-DNA binding significantly influences binding preferences of the majority of transcription regulators in promoter regions of the yeast genome. We show that promoters of SAGA-dominated and TFIID-dominated genes can be statistically distinguished based on the landscape of nonspecific protein-DNA binding free energy. In particular, we predict that promoters of SAGA-dominated genes possess wider regions of reduced free energy compared to promoters of TFIID-dominated genes. We also show that specific and nonspecific TF-DNA binding are functionally linked and cooperatively influence gene expression in yeast. Our results suggest that nonspecific TF-DNA binding is intrinsically encoded into the yeast genome, and it may play a more important role in transcriptional regulation than previously thought.
authors: Department of Chemistry, Ben-Gurion University of the Negev, Be'er-Sheva, Israel.
authors: Ariel
authors: A
authors: Afek
authors: David B
authors: DB
authors: Lukatsky
mesh_terms: D001665:Binding Sites; D004271:DNA, Fungal / Q000378:metabolism*; D019277:Entropy; D005656:Fungal Proteins / Q000378:metabolism*; D016681:Genome, Fungal / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D013379:Substrate Specificity; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D004271:DNA, Fungal; D005656:Fungal Proteins; D014157:Transcription Factors