Figure 7

Sequence context effects were not determined by individual nucleotides. (A) Sequence logos for a sample of promoters with a center-to-center distance of 20 bp between Cbf1 and Met31/32 binding sites. At each position, the height of the nucleotide corresponds to the information content at that position, which weights its frequency in the sequenced sample compared with its expected frequency [31]. The sample was divided into sequences that supported or inhibited gene activation, as well as whether a guanine or thymine was found adjacent to the Met31/32 binding site. A separate logo was generated by WebLogo for each sub-sample [30]. Since three invariant nucleotides on both the 5' and 3' ends of the spacer sequence represented the Cbf1 and Met31/32 binding sites, respectively, only the central 14 bp are displayed. (B) Mutation of single nucleotides in positive promoters failed to inhibit reporter gene activation in vivo. Each column corresponds to a yeast strain containing a different spacer sequence with a distance of 20 bp between the binding sites. The clone number and nucleotide at position 11 are indicated above each panel. Ten-fold serial dilutions were performed in triplicate, and a representative dilution is shown.