Comparison of translocation and intrachromosomal breakpoint junctions. (A) Strategy to compare translocations and intrachromosomal repair at the same sequence. For translocations, I-SceI was expressed in the p5rE cell line, and for intrachromosomal repair, I-SceI was expressed in 2 p5rE translocation clones that re-established the I-SceI site on der(17) but not on der(14). After transfection, neo⁺ cells were selected in G418, and genomic DNA was digested with I-SceI prior to PCR amplification with the indicated primers. PCR products were cloned and sequenced. (B) Comparison of deletion lengths at translocation and intrachromosomal breakpoint junctions. The 53 intrachromosomal and 36 of the translocation junctions from p5rE der(17) were isolated by the PCR strategy shown in panel A; 38 translocation junctions from individually isolated p5rE neo⁺ clones that had not re-established the I-SceI site also are shown for der(17). (C) Comparison of microhomology distributions for translocation and intrachromosomal breakpoint junctions. The translocation junctions are compiled from the PCR strategy shown in panel A and neo⁺ clonal analysis for p5rE der(17). Only junctions containing simple deletions are included.