Translocation breakpoint junctions have similar characteristics in wild-type, Xrcc4−/− mutant and complemented cells, and Ku70−/− cells. (a) Representative der(17) translocation junction sequences obtained from Xrcc4−/− and Xrcc4-complemented cells. DNA ends generated by I-SceI on chrs.17 and 14 are indicated in red and blue, respectively. A summary of the various end modifications is presented to the left of each junction in bp: Δ, total deletion; µ, microhomology; +, insertion. Sequences are annotated as follows: del, deletion length from the DNA end; underline, microhomology; +, length of long insertion. The middle green sequences are short insertions from chr. 14; considering a template model for their insertion, the sequences in red shading (TAA) would be microhomology between the DNA ends that could anneal to act as a primer and the blue shading would represent microhomology for annealing after DNA synthesis between the 2 DNA ends (see text). (b) Deletion lengths for der(17) breakpoint junctions. Each value represents the combined deletion from both ends of an individual junction. The median deletion length for each genotype is indicated by a bar on the graph and the value is give below the graph. Deletion lengths do not differ significantly from each other (two-tailed Mann-Whitney test). +X4, transient complementation with Xrcc4. (c) Microhomology and insertion frequencies are similar for the four genotypes. (d) Distribution of microhomology lengths for der(17) breakpoint junctions. Only junctions with simple deletions (i.e., without an insertion) are included. (e) Lack of correlation between deletion length and microhomology use. Only junctions for Xrcc4−/− cells are plotted.