MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings

Abstract

DNA double-strand breaks are normal consequences of cell division and differentiation and must be repaired faithfully to maintain genome stability. Two mechanistically distinct pathways are known to efficiently repair double-strand breaks: homologous recombination and Ku-dependent non-homologous end joining. Recently, a third, less characterized repair mechanism, named microhomology-mediated end joining (MMEJ), has received increasing attention. MMEJ repairs DNA breaks via the use of substantial microhomology and always results in deletions. Furthermore, it probably contributes to oncogenic chromosome rearrangements and genetic variation in humans. Here, we summarize the genetic attributes of MMEJ from several model systems and discuss the relationship between MMEJ and 'alternative end joining'. We propose a mechanistic model for MMEJ and highlight important questions for future research.

Figure 1

Comparison of NHEJ, MMEJ and SSA pathways in S. cerevisiae. During NHEJ repair of a DSB, the Ku70–Ku80 heterodimer binds, preventing DNA end resection. Repair proceeds by annealing at short microhomologies (green boxes), fill-in by Pol4 and ligation using DNA ligase IV, resulting in small deletion and insertion products. Both MMEJ and SSA require end resection or unwinding to reveal homologous sequences, although the length of homology required for MMEJ (5–25 bp) is shorter than for SSA. SSA and MMEJ also require 3′ flap cleavage before fill-in synthesis and ligation. Whereas MMEJ products can contain inserted nucleotides, these are never observed in SSA. Notably, although the three pathways share some common genetic requirements, overall they are distinct (Table 1).

Figure 2

Model for MMEJ and alternative end-joining repair. During the initial stages of MMEJ, Ku70–Ku80 (green) and Rad51 (red), which inhibit MMEJ, are prevented from binding or are removed. This enables 5––3′ resection by the MRX complex, Sae2 and Exo1 (indicated by dark red partial circle) that reveals microhomologous sequences (blue boxes). These microhomologies transiently and dynamically anneal to each other. (i) In cases in which the annealing is stable, repair is completed by flap trimming, fill-in DNA synthesis and ligation, resulting in a deletion relative to the original sequence. Mismatch repair is not required for MMEJ, although it might have a supporting role. (ii) Alternatively, one or more translesion polymerases (yellow) can extend the annealed sequences (represented here by orange–blue boxes) using templated error-prone synthesis. Dissociation of the initial microhomologies and realignment at other microhomologous sequences, followed by flap trimming, fill-in DNA synthesis and ligation completes repair, resulting in a deletion plus insertion event. Many variations and iterations of (ii) can hypothetically occur, resulting in complex insertion–deletion junctions.