Figure 4.

Multiple Repair Pathways Active at One Locus

(A and B) The spectrum of indels and their frequencies at the LBR2 locus at time point t = 60 hr in cells cultured without (A) or with (B) 1 μM NU7441. A representative experiment is shown. Light-blue bar, wild-type sequence; dark-blue bars, indels.

(C) Frequencies of −7 and +1 indels in the presence (black, n = 7) and absence (gray, n = 4) of NU7441. All series are normalized to the total indel fraction. Asterisks indicate p values according to Student’s t test: ^∗p < 0.05; ^∗∗p < 0.005; ^∗∗∗p < 0.0005.

(D) The −7 deletions consist of two types; red nucleotides mark the deleted DNA. Shaded nucleotides show possible models for microhomology-mediated repair. Percentages indicate the proportion of observed −7 sequence reads.

(E) TIDE analysis of +1 insertion and −7 deletion indels after exposure of the cells to 10 Gy of IR at the time of Cas9 induction. Asterisks indicate p values according to Student’s t test: ^∗p < 0.05; ^∗∗p < 0.005; ^∗∗∗p < 0.0005.