Fig. 4. Promoter Context Effects.

A Measured in vivo transcription rates for the J23101 promoter genetic part with varied upstream (UP) and downstream (ITR) sequences, showing transcriptional context effects. Gray dots denote independent measurements (n = 4 biological replicates). Bars denote each variants measured mean ± standard deviation. B Transcriptional context effects are quantified for common promoter genetic parts, showing predicted transcription rates when varying 30 bp of the upstream and downstream sequences. Distributions were created using 10,000 simulations (n = 10,000). Box bounds were defined by the first and third quartiles of the distribution, center lines by the median, whiskers by the minima and maxima, and black dots by outliers. C Model predictions are compared to in vivo fluorescence measurements for these promoters when specifying their upstream and downstream sequences (R² = 0.79, Spearman’s ρ = 0.85). Data are provided in Supplementary Data 1.