title: Flexible promoter architecture requirements for coactivator recruitment.
abstract: BACKGROUND
  The spatial organization of transcription factor binding sites in regulatory DNA, and the composition of intersite sequences, influences the assembly of the multiprotein complexes that regulate RNA polymerase recruitment and thereby affects transcription. We have developed a genetic approach to investigate how reporter gene transcription is affected by varying the spacing between transcription factor binding sites. We characterized the components of promoter architecture that govern the yeast transcription factors Cbf1 and Met31/32, which bind independently, but collaboratively recruit the coactivator Met4.
  
  
  RESULTS
  A Cbf1 binding site was required upstream of a Met31/32 binding site for full reporter gene expression. Distance constraints on coactivator recruitment were more flexible than those for cooperatively binding transcription factors. Distances from 18 to 50 bp between binding sites support efficient recruitment of Met4, with only slight modulation by helical phasing. Intriguingly, we found that certain sequences located between the binding sites abolished gene expression.
  
  
  CONCLUSIONS
  These results yield insight to the influence of both binding site architecture and local DNA flexibility on gene expression, and can be used to refine computational predictions of gene expression from promoter sequences. In addition, our approach can be applied to survey promoter architecture requirements for arbitrary combinations of transcription factor binding sites.
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. dchiang@ocf.berkeley.edu
authors.forename: Derek Y
authors.initials: DY
authors.lastname: Chiang
authors.forename: David A
authors.initials: DA
authors.lastname: Nix
authors.forename: Ryan K
authors.initials: RK
authors.lastname: Shultzaberger
authors.forename: Audrey P
authors.initials: AP
authors.lastname: Gasch
authors.forename: Michael B
authors.initials: MB
authors.lastname: Eisen
mesh_terms: D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / Q000235:genetics; D050976:Basic-Leucine Zipper Transcription Factors / Q000235:genetics; D001665:Binding Sites; D015966:Gene Expression Regulation, Fungal; D015723:Gene Library; D008957:Models, Genetic; D010957:Plasmids / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000502:physiology*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics
chemical_list: D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; D050976:Basic-Leucine Zipper Transcription Factors; C064042:CBF1 protein, S cerevisiae; C073675:MET4 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors