title: A global view of the selection forces in the evolution of yeast cis-regulation.
abstract: The interaction between transcription factors and their DNA binding sites is key to understanding gene regulation. By performing a genome-wide study of the evolutionary dynamics in yeast promoters, we provide a first global view of the network of selection forces in the evolution of transcription factor binding sites. This analysis gives rise to new models for binding site activity, identifies families of related binding sites, and characterizes the functional similarities among them. We discovered rich and highly optimized selective pressures operating inside and around these families. In several cases, this organization reveals that a single transcription factor has multiple functional modes. We demonstrate how such functional heterogeneity is related to the binding site's affinity and how it is exploited in transcription programs.
authors.affiliation: School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel. amos@tau.ac.il
authors.forename: Amos
authors.initials: A
authors.lastname: Tanay
authors.forename: Irit
authors.initials: I
authors.lastname: Gat-Viks
authors.forename: Ron
authors.initials: R
authors.lastname: Shamir
mesh_terms: D001665:Binding Sites / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D019143:Evolution, Molecular; D015966:Gene Expression Regulation, Fungal / Q000235:genetics*; D008957:Models, Genetic; D016296:Mutagenesis / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D012440:Saccharomyces / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012641:Selection, Genetic; D014157:Transcription Factors / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D004271:DNA, Fungal; D014157:Transcription Factors