Fig. 6: Predictive rules enable endogenous activation.

a CRISPRa using dCas9 and dxCas9(3.7) was targeted to a yajG reporter plasmid from the E. coli promoter collection³⁶. Three scRNA target sites were selected; two sites were located at the positions where CRISPRa was most effective (Y1–2), and one was located out of phase (Y3). A negative control (OT) expressing an off-target scRNA (J306) was included. b CRISPRa was targeted to yajG and five additional promoters from the E. coli promoter collection (Supplementary Methods). Two scRNA sites located at the positions where CRISPRa was most effective were targeted for each gene using dxCas9(3.7). Samples are arranged by baseline expression of the target genes, in ascending order left to right. Fold activation indicates the median fluorescence of strains relative to an off-target control (J306). Values a and b represent the average±standard deviation calculated from n = 3 biologically independent samples. Stars indicate a statistically significant difference from the off-target control using a two-tailed unpaired Welch’s t test (*p-value < 0.05, **p value < 0.01). Exact p values: E1: 0.036, E2: 0.024, B1: 0.031, B2: 0.141, P1: 0.033, P2: 0.021, D1: 0.088, D2: 0.585, U1: 0.0008, U2: 0.001, Y1: 0.013, Y2: 0.003. Source data are provided as a Source Data file.