Figure 5. The Different Outcomes of Annealing-Dependent Error-Prone Double-Strand Break (DSB) Repair.

After formation of a DSB, DNA resection results in two single-stranded overhangs and exposure of DNA homology. SSA uses annealing of large DNA sequences of homology, which leads to deletions of large fragments of DNA. By contrast, alt-EJ requires pairing of only small homologous DNA sequences (microhomologies), which can lead to deletions and/or insertions depending on how the repair is orchestrated: (i) When the annealing is stable the overhanging noncomplementary flaps are trimmed by the endonuclease complex and repair is completed by fill-in DNA synthesis and ligation, resulting in deletions of the DNA regions flanking the original break. (ii) Alternatively, translesion polymerases (such as Polυ) may extend the annealed sequences using untemplated error-prone DNA synthesis resulting in realignment at newly created micro-homologous sequences. Then the repair is completed by flap trimming, gap-filling DNA synthesis, and ligation, which results in a deletion plus insertion junction. (iii) Flap trimming followed by untemplated DNA error-prone synthesis can generate new regions of microhomology leading to insertions of DNA sequences. Abbreviations: alt-EJ, alternative end joining; DSB, double-strand break; SSA, single-strand annealing.