title: Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus.
abstract: Gene expression evolution occurs through changes in cis- or trans-regulatory elements or both. Interactions between transcription factors (TFs) and their binding sites (TFBSs) constitute one of the most important points where these two regulatory components intersect. In this study, we investigated the evolution of TFBSs in the promoter regions of different Saccharomyces strains and species. We divided the promoter of a gene into the proximal region and the distal region, which are defined, respectively, as the 200-bp region upstream of the transcription starting site and as the 200-bp region upstream of the proximal region. We found that the predicted TFBSs in the proximal promoter regions tend to be evolutionarily more conserved than those in the distal promoter regions. Additionally, Saccharomyces cerevisiae strains used in the fermentation of alcoholic drinks have experienced more TFBS losses than gains compared with strains from other environments (wild strains, laboratory strains, and clinical strains). We also showed that differences in TFBSs correlate with the cis component of gene expression evolution between species (comparing S. cerevisiae and its sister species Saccharomyces paradoxus) and within species (comparing two closely related S. cerevisiae strains).
authors.affiliation: Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan National Yang-Ming University, Taipei, Taiwan Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Schaefke
authors.affiliation: National Yang-Ming University, Taipei, Taiwan.
authors.forename: Tzi-Yuan
authors.initials: TY
authors.lastname: Wang
authors.affiliation: National Yang-Ming University, Taipei, Taiwan.
authors.forename: Chuen-Yi
authors.initials: CY
authors.lastname: Wang
authors.affiliation: National Yang-Ming University, Taipei, Taiwan China Medical University Hospital, Taichung, Taiwan Department of Ecology and Evolution, University of Chicago whli@gate.sinica.edu.tw.
authors.forename: Wen-Hsiung
authors.initials: WH
authors.lastname: Li
mesh_terms: D001665:Binding Sites; D019143:Evolution, Molecular; D015870:Gene Expression; D011401:Promoter Regions, Genetic; D012440:Saccharomyces / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors
keywords:  cis evolution; natural selection; regulatory evolution; selective constraint; trans evolution; yeast