Fig. 1: Investigation of COMET promoter design rules.

a The schematic shows the modular, tunable features of COMET TFs and promoters. b Five ZFa with different ZF domains all induced reporter expression (one-tailed Welch’s t-test: *p < 0.05, **p < 0.01, ***p < 0.001). c Increasing the number of ZF binding sites increased the level of gene expression in the presence of ZFa (ANOVA p < 0.001) but not without ZFa (ANOVA p = 0.24). Reporter expression increased significantly from 6 to 8 and from 8 to 10 binding sites but not on either side of this range (Tukey’s HSD test with α = 0.05). d Moving the ZF binding site array farther upstream of the TATA box reduced reporter expression (two-factor ANOVA p < 0.001), and arrays with more binding sites showed more substantial decreases in reporter expression. e Compaction of ZFa binding sites enhanced ZFa-induced reporter expression, for an equivalent number of ZF binding sites (one-tailed Welch’s t-test, p = 0.002), and across compact promoters, ZFa-induced reporter expression increased with the number of binding sites (ANOVA p < 0.001). Reporter expression increased significantly from 2 to 3, 3 to 4, 5 to 6, and 8 to 12 binding sites (Tukey’s HSD test with α = 0.05). Experiments were conducted in biologic triplicate, and data were analyzed as described in Methods. Error bars represent the S.E.M. Source data are provided in the Source Data file.