Mammalian non-homologous DNA end joining (NHEJ) is the primary pathway for the repair of DNA double-strand breaks (DSBs) throughout the cell cycle, including during S and G2 phases.
NHEJ relies on the Ku protein to thread onto each broken DNA end. Ku recruits the enzymes and complexes that are needed to trim (nucleases) or to fill in (polymerases) the ends to make them optimally ligatable by the DNA ligase IV complex.
The configuration of the DNA ends determines which of several subpathways of NHEJ is able to join the ends. Because NHEJ is flexible and iterative, any of these subpathways can be used but some pathways are more efficient than others for certain DNA ends.
When NHEJ is absent owing to a lack of Ku or the DNA ligase complex, alternative end joining (a-EJ) can join the ends using microhomology (usually >4 bp) and there is often some evidence of templated insertions of substantial length (>10 nucleotides). DNA polymerase θ (Pol θ) is of key importance for a-EJ.
The single-strand annealing (SSA) pathway requires further end resection by exonuclease 1 (EXO1), Bloom syndrome RecQ-like helicase (BLM) or DNA replication helicase/nuclease 2 (DNA2) to generate the long 3′ single-strand DNA (ssDNA) tails (>20 nucleotides) that are bound by replication protein A (RPA) to prevent the formation of DNA secondary structures. The 3′ ssDNA tails are annealed by RAD52.
DNA double-strand breaks (DSBs) are the most dangerous type of DNA damage because they can result in the loss of large chromosomal regions. In all mammalian cells, DSBs that occur throughout the cell cycle are repaired predominantly by the non-homologous DNA end joining (NHEJ) pathway. Defects in NHEJ result in sensitivity to ionizing radiation and the ablation of lymphocytes. The NHEJ pathway utilizes proteins that recognize, resect, polymerize and ligate the DNA ends in a flexible manner. This flexibility permits NHEJ to function on a wide range of DNA-end configurations, with the resulting repaired DNA junctions often containing mutations. In this Review, we discuss the most recent findings regarding the relative involvement of the different NHEJ proteins in the repair of various DNA-end configurations. We also discuss the shunting of DNA-end repair to the auxiliary pathways of alternative end joining (a-EJ) or single-strand annealing (SSA) and the relevance of these different pathways to human disease.
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The authors thank R. Mosteller for comments on the manuscript. Work in the authors' laboratory is supported by the US National Institutes of Health (NIH) (M.R.L.) and by the Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT) (15H04323 to N.A.).
The authors declare no competing financial interests.
Abundance of key proteins involved in nonhomologous DNA end joining (NHEJ), alternative end joining (a-EJ), single-strand annealing (SSA) and homologous recombination (HR). (PDF 399 kb)
The same DSB can be repaired in many different ways, depending on the order in which NHEJ proteins act. (PDF 200 kb)
- V(D)J recombination
DNA recombination process during B or T lymphocyte activation in which the antigen receptors variable domain exons are assembled from sub-exonic segments called V, D and J to ultimately generate an immunoglobulin gene or T cell receptor, respectively.
- Immunoglobulin heavy chain class switch recombination
The DNA recombination process by which the immunoglobulin heavy chain isotype is changed from producing IgM to producing IgG, IgA or IgE.
One or more base pairs of complementarity at the two DNA ends of a break.
- FAT domain
FRAP (FKBP12-rapamycin-associated protein), ATM (ataxia telangiectasia mutated), TRRAP (transformation/transcription domain-associated protein) domain. A structural domain found in phosphatidylinositol 3-kinase-like kinase family members.
- Pol X family polymerases
Subfamily of DNA polymerases; based on homology it includes Pol β, Pol μ, Pol λ and terminal deoxynucleotidyltransferase (TdT).
- BRCA1 C terminus
(BRCT). Protein domain of approximately 100 aa that binds to phosphoproteins that are often involved in the DNA damage response.
- DNA end breathing
Break of the hydrogen bonds between one or more base pairs in the anti-parallel strands of the DNA duplex break.
- Templated insertions
Nucleotide additions at a double-strand break repair junction that seem to be direct or inverted repeat copies derived from either strand of either of the two DNA ends.
Shattering of chromosomal regions followed by random repair of the DNA fragments in some human neoplasms and inherited disorders.
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Chang, H., Pannunzio, N., Adachi, N. et al. Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nat Rev Mol Cell Biol 18, 495–506 (2017). https://doi.org/10.1038/nrm.2017.48
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