How cells ensure correct repair of DNA double-strand breaks

Abstract

DNA double-strand breaks (DSBs) arise regularly in cells and when left unrepaired cause senescence or cell death. Homologous recombination (HR) and nonhomologous end-joining (NHEJ) are the two major DNA-repair pathways. Whereas HR allows faithful DSB repair and healthy cell growth, NHEJ has higher potential to contribute to mutations and malignancy. Many regulatory mechanisms influence which of these two pathways is used in DSB repair. These mechanisms depend on the cell cycle, post-translational modifications, and chromatin effects. Here, we summarize current research into these mechanisms, with a focus on mammalian cells, and also discuss repair by "alternative end-joining" and single-strand annealing.

Keywords: BRCA1; DNA damage; DNA repair; chromatin; double-strand break; homologous recombination; nonhomologous end-joining; ubiquitylation (ubiquitination).

Figure 1.

Overview of pathways for DNA DSB repair in mammals. Canonical nonhomologous end-joining (C-NHEJ) involves direct ligation at the break site, often with some number of base insertions or deletions that can cause mutation. A-EJ refers to NHEJ that does not use canonical end-joining factors. Homologous DNA sequences are indicated in red. A-EJ often involves some degree of resection, creating single-stranded regions that may pair at areas of micro-homology. Processing and excision of the intervening sequence is likely to cause mutation at the repair junction. SSA also involves resection and pairing of homologous regions but uses different repair machinery and is more likely to result in large deletion mutations. HR involves resection at the DSB and repair using a homologous DNA sequence as a template. It is usually error-free but may occasionally contribute to mutation. For more details see Refs. and .

Figure 2.

Cell cycle-dependent regulation of DSB repair pathways in mammals. Pathways for repair of DSBs are active at different rates at different phases of the cell cycle. NHEJ dominates in G₁, whereas HR is most active in S phase. NHEJ and HR appear to compete for repair of DSBs in G₂, but both pathways are down-regulated during M phase. Changes in activity of different pathways depend on differential expression of regulatory factors and post-translational modification. Several regulatory mechanisms are shown. See text for details.

Figure 3.

53BP1-BRCA1 network for regulation of repair pathway choice at DSBs. 53BP1 normally represses use of HR for repair of DSBs. This is achieved in part by 53BP1-mediated recruitment of the downstream regulators RIF1, REV7, and PTIP. These factors repress resection, including by recruitment of Artemis, which can remove potentially-recombinogenic tracts of single-stranded DNA at the break site. The effect of 53BP1 is antagonized by factors that compete for chromatin-binding sites (JMJD2A, L3MBTL, and RNF169), inhibit 53BP1 recruitment (TIP60 and TIRR), block recruitment of downstream modulators of 53BP1 (SCAI), or promote degradation of 53BP1 (UBCH7). BRCA1 recruited to break sites via RAP80 may not always be in a complex that supports HR, but interaction with ZMYM3 may contribute to activation of BRCA1 to promote HR. BRCA1 antagonizes 53BP1 in part through recruitment of UHRF, which ubiquitylates RIF1, preventing RIF1 from being stably retained at the break site. BRCA1 may also inhibit 53BP1 binding through E3 ubiquitin ligase activity at the break. See text for more details.

Figure 4.

Chromatin and nuclear positioning contribute to DSB repair pathway choice. H3K36Me₃ and acetylated histones are present in transcriptionally-active regions. These marks promote use of HR for repair of DSBs by LEDGF-mediated recruitment of CtIP and ZMYND8-mediated recruitment of the NuRD complex, which remodels nucleosomes. The presence of macro-H2A also correlates with increased use of HR. Heterochromatic regions of the genome, particularly pericentromeric heterochromatin, are preferentially repaired by HR. Conversely, DSBs that occur near the nuclear periphery show increased repair by NHEJ. See text for details.