The effect on expression of TATA-box and Initiator (Inr) combinations and relative distances in different backgrounds. (A) Comparison of expression levels of synthetic oligos with TATA to those containing both TATA and Inr. Each dot represents a pair of sequences with either TATA or TATA+Inr elements. An increase in expression is observed when adding Inr (P < 10−3, Wilcoxon signed-rank test). (B) Testing for synergy between TATA and Inr elements. Each dot represents a pair of expression values. On the x-axis, expression was computed as the sum of the expression of separate oligos with either TATA or Inr. The y-axis represents expression measurements of oligos that contain the two elements. (C–E) Comparison of oligos with either TATA, Inr, or TATA+Inr in three different promoter backgrounds. Presented P-values were computed by Wilcoxon rank-sum test (n = 16 in each group). (F–H) Testing the effect of the distance between the TATA and the Inr in three different backgrounds. We designed oligos in which we placed the Inr in its consensus position and systematically changed the location of the TATA (2- to 3-nt increments). Each blue dot represents the expression level at a single position. The consensus position of the TATA (−31) is denoted.
