Flexible promoter architecture requirements for coactivator recruitment

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.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.In most eukaryotes, the sequences that regulate transcription integrate multiple signals, through the binding of different transcription factors, to modulate levels of gene expression. When bound to DNA, transcription factors anchor the assembly of multiprotein complexes that influence the recruitment of RNA polymerase. Efficient assembly depends on optimally spaced protein-protein interactions among transcription factors and auxiliary proteins [1-4]. Since transcription factors recognize specific sites on DNA, the distance between these binding sites can influence how transcription factors interact with each other and other proteins. For example, overlapping sites may prevent two transcription factors from binding simultaneously, while sites too distant from each other may hinder bound transcription factors from recruiting necessary cofactors. Furthermore, some distantly spaced sites can only properly interact when the DNA between them is looped, a process influenced by the composition of the looped DNA.Computational approaches take into account the multifactorial nature of transcriptional regulation when discovering transcription facto