Microhomology-mediated end joining: Good, bad and ugly

Abstract

DNA double-strand breaks (DSBs) are induced by a variety of genotoxic agents, including ionizing radiation and chemotherapy drugs for treating cancers. The elimination of DSBs proceeds via distinctive error-free and error-prone pathways. Repair by homologous recombination (HR) is largely error-free and mediated by RAD51/BRCA2 gene products. Classical non-homologous end joining (C-NHEJ) requires the Ku heterodimer and can efficiently rejoin breaks, with occasional loss or gain of DNA information. Recently, evidence has unveiled another DNA end-joining mechanism that is independent of recombination factors and Ku proteins, termed alternative non-homologous end joining (A-NHEJ). While A-NHEJ-mediated repair does not require homology, in a subtype of A-NHEJ, DSB breaks are sealed by microhomology (MH)-mediated base-pairing of DNA single strands, followed by nucleolytic trimming of DNA flaps, DNA gap filling, and DNA ligation, yielding products that are always associated with DNA deletion. This highly error-prone DSB repair pathway is termed microhomology-mediated end joining (MMEJ). Dissecting the mechanisms of MMEJ is of great interest because of its potential to destabilize the genome through gene deletions and chromosomal rearrangements in cells deficient in canonical repair pathways, including HR and C-NHEJ. In addition, evidence now suggests that MMEJ plays a physiological role in normal cells.

Keywords: Chromosome rearrangement; DNA double strand break; End joining; Microhomology; Mutagenesis.

Fig. 1.

The basic mechanisms of MMEJ in human cells. MMEJ could be divided to three discrete steps, pre-annealing, annealing, and post-annealing of the flanking MHs. PARP1 binds to DSB ends and facilitates the recruitment of resection factors [CtIP and Mre11 complex (Mre11/Rad50/Nbs1)] to uncover MHs (shown in yellow boxes) flanking DSBs. MHs that are far from the break likely require extensive resection by BLM/EXO1 to facilitate MMEJ. Annealing of MHs, which is inhibited by single strand binding RPA complex, induces the formation of non-homologous tails/flaps. Non-homologous tails/flaps are then removed by XPF/ERCC1 nuclease before filling-in synthesis and ligation by Polθ and LigI/III, respectively. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 2.

Genomic instability caused by DNA DSB repair mechanisms. C-NHEJ (i) generates small sequence deletions/insertions at breakpoint junctions. MMEJ (ii) induces deletions and insertions at the breakpoint junctions and hypermutagenesis at the flanking DNA sequence up to several kilobases from the break. Both C-NHEJ and MMEJ could trigger chromosomal translocations and telomeric fusions. SSA (iii) also induces large deletions but not insertions at repair junctions. In BIR (iv) and gene conversion (v), low fidelity DNA synthesis produces mutagenesis at the flanking DNA sequence and could induce chromosomal translocations if recombination involves non-allelic template and/or crossover formation. Blue boxes represent homologies and the stars represent mutations. The dotted lines are newly synthesized DNA. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)