Fig. 2: Prime editing with stably expressed PEmax and epegRNA sensor libraries achieves high-efficiency precision editing.
From: A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening
a, Schematic of self-targeting expression cassette. Regions indicated with purple varied coordinately across the library (as denoted by dots), with dark purple specifying variable epegRNA components and light purple specifying the corresponding target site. mU6, modified mouse U6 promoter. b, Schematic of workflow for sensor screens. c, Percentages of sequencing reads from sensor targets containing only the precise edit from two replicates of +5 G>H screens performed in PEmax (top) or PEmaxKO (bottom) cells, at day 28 post transduction. Each data point represents an individual epegRNA–target pair. Correlation between replicates (Pearson’s r) indicated. Density plots on top and side show data distribution for replicates 1 and 2, respectively. d, Replicate-averaged percentages of sequencing reads from sensor targets containing only the precise edit for experimental (noncontrol) epegRNA–target pairs from +5 G>H screen performed in PEmax cells, at indicated days post transduction (n = 635, 630 and 633 pairs per day for G>A, G>C and G>T edits, respectively). Median and interquartile range (IQR) of the full set of experimental epegRNA–target pairs installing specified substitution types on indicated days are shown. Whiskers extend 1.5× IQR past the upper and lower quartiles. e, As in d, but for +5 G>H screen performed in PEmaxKO cells. f, Replicate-averaged percentages of sequencing reads from sensor targets containing only the precise edit for experimental epegRNA–target pairs from +5 G>H screens performed in PEmax and PEmaxKO cells, at day 28 post transduction. Density plots on top and side show data distribution per substitution type for PEmax and PEmaxKO cells, respectively. g, Maximum precise editing frequencies (replicate-averaged) among multiple epegRNA designs for each edit in the Tiled edits screen performed in PEmaxKO cells, at day 10 post transduction. Each data point represents a unique edit (n = 195), binned by edit position relative to the Cas9(H840A) nick. Boxplots indicate the median and IQR for each group with whiskers extending 1.5× IQR past the upper and lower quartiles. h, As in g, but binned by substitution type. b, Created with BioRender.com.
