FIG 1.

CRISPRi induction reduces fitness when targeting essential genes. (A) Schematic of the E. coli CRISPRi system showing the integration sites and promoters of the sgRNA and dcas9 constructs. (B) CRISPRi targeting rfp expression achieved titratable and unimodal knockdown at various IPTG levels. The red histograms correspond to 0, 0.03125, 0.0625, 0.125, and 1 mM IPTG. No RFP (rfp-) or full RFP expression (sgRNA-) is indicated in black. (C and D) Gaussian kernel density estimate of the distribution of relative fitness values for strains targeting essential (black) and nonessential (gray) genes with the CRISPRi system at basal induction (C) and full induction using 1 mM IPTG (D). The solid red line indicates the median of 48 nontargeting controls, and the dashed red lines indicate ±3 standard deviations (SD) from the median, estimated from the median absolute distance.