Figure 3.
Combined effects of sequence context and genotype on deletion boundary frequency. Frequency as percentage of total repair products of deletion boundaries associated with net insertions (black), junctional microhomologies (gray) and apparent blunt joins (white) in wild-type, lig4 and polQ genetic backgrounds. ‘Deletion boundary’ is defined as the position (including any junctional microhomologies) where an uninterrupted match between the original sequence and the repair product resumes. X-axis indicates top strand sequence. Deletions extending beyond the sequence shown are represented by a plus sign (+). (a–c) Boundaries of deletions to the right of the bottom strand nick. The underlined sequence (GGCC) is the left half of a GGCC repeat. Arrows show clustering of deletion boundaries at this repeat in wild-type and lig4 but not polQ sequences. (d–f) Deletion boundaries to the left of the top strand nick. The underlined sequence (TTA) is a 3 bp direct repeat. Note different overall shape of the histograms of deletion boundaries to the right and left of the DSB in all genotypes (compare a–c, d–f). Arrows show virtual absence of 2 bp deletions in wild-type and lig4 but not polQ sequences. WT: n = 70; lig4: n = 83; polQ: n = 57.