Extended Data Fig. 6: epegRNAs do not show systemic CRISPRi effect.

a, Replicate-averaged growth phenotypes for stop and spacer- and codon-matched synonymous epegRNAs from StopPR screen at day 14 post transduction of library, for the subset in which the matched synonymous epegRNA targets a + 5-6 position (PAM-disrupting). b, Replicate-averaged growth phenotypes for stop, spacer- and codon-matched synonymous, and no edit epegRNAs from StopPR screen at day 14 post transduction of library. epegRNAs grouped by distance to the closest transcription start site (TSS) annotated in the targeted gene. Number of epegRNAs in each group denoted above as n. Two-sided t-test p-values comparing phenotypes between relevant groups reported in Supplementary Table 6. Median and interquartile range (IQR) of the set of epegRNAs targeting indicated distances from the TSS are shown, excluding epegRNAs targeting the D-1 position (see section “Unbiased identification of splice site variants”). Whiskers extend 1.5*IQR past the upper and lower quartiles. c, Replicate-averaged growth phenotypes for stop and spacer- and codon-matched synonymous epegRNAs (excluding D-1 epegRNAs) from StopPR screen at day 14 post transduction of library, for the subset in which the matched synonymous epegRNA targets a non-PAM-disrupting position within the indicated distance from the TSS. Non-PAM-disrupting synonymous epegRNAs target a non +5-6 position and could allow for continued target engagement after editing. epegRNAs targeting closest to the TSS are most expected to show CRISPRi activity, if present²⁹. d, As in c, but for the subset in which the matched synonymous epegRNA targets a PAM-disrupting position within the indicated distance from the TSS. e, Fold change of cells expressing epegRNAs over two weeks post transduction of epegRNAs (determined by loss of co-expressed BFP). Analysis for 6 synonymous epegRNAs disrupting D-1 splice sites and spacer-matched no edit control epegRNAs. Data for n = 3 independent biological replicates shown, lines and error bars represent mean +/- s.d. Dotted lines in a-d denote phenotype cutoffs (Z < -2).