Fig. 2: WGS after transient MMR inhibition in embryos.

a, Percentages of total reads containing the precise +5 G > A edit (blue) or errors (orange) in Chd2 from ear clips of 2- to 3-week-old mice developed from embryos microinjected with PE4 components (PE2 editor mRNA, pegRNA, mMLH1dn mRNA) at the two-cell stage. Data compiled from multiple experiments (Supplementary Table 13 and Methods). b, Pedigree of ‘PE4 family’ (top). Black indicates the ‘treated’ group of select progeny microinjected at the two-cell stage with PE4 components (PE2 editor mRNA, Chd2 + 5 G > A pegRNA, mMLH1dn mRNA). Unshaded family members indicate mice/embryos treated as the ‘control’ group, including sibling progeny microinjected at the two-cell stage with PE2 editor mRNA only. Percentages indicate precise edit efficiency at E12.5 as determined by WGS. Plot (bottom) compares editing frequencies in treated embryos across sequencing methods (target versus whole-genome sequencing). Superscripts denote individual progeny from ‘PE4 family’. Dashed line represents x = y. c, Total unique SNVs (left) and total unique indels (right) detected in members of the ‘PE4 family’ after joint genotyping (black line indicates mean from each group, P values from two-sided Welch’s t-tests). d, Cumulative frequencies of unique SNVs (left) or unique indels (right) by type for members of the ‘PE4 family’. F, female; M, male. e, Fraction of unique −1 bp deletions directly adjacent to poly(A/T) nucleotide tracts in treated and control mice/embryos from each indicated family (P values from two-sided Welch’s t-test). Treated and control groups are defined in b and f. f, Pedigrees of additional mouse families. Black denotes treated groups. Unshaded siblings comprise control groups. For the ‘PE2* family’ (left), treated embryos were microinjected with PE2* components (PEmax mRNA, Chd2 + 5 G > A pegRNA) at the two-cell stage, whereas control embryos were microinjected with pegRNA only. For the ‘mMLH1dn family’ (right), treated embryos were microinjected with mMLH1dn mRNA and the Chd2 + 5 G > A pegRNA (but no editor) at the two-cell stage, whereas control embryos were microinjected with pegRNA only. One control embryo (not indicated) was omitted from analysis for this family after sequencing failed quality control (Methods). Percentages indicate precise edit efficiency in treated embryos at E12.5. g, Number of unique indels detected in treated embryos in each family (n = 3, PE4 family; n = 2, PE2* family; n = 3, mMLH1dn family) relative to the average of control mice/embryos from the same family. Data points represent fold-change for individual mice/embryos. Bars indicate the mean difference. For pedigree diagrams, red dashed boxes indicate mice/embryos subjected to WGS. For box plots, boxes indicate the median and IQR of each group with whiskers extending 1.5 × IQR (a) and 2 × IQR (e) past the upper and lower quartiles.