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. 2012;2(3):249-68.
Epub 2012 Apr 21.

Initiation of DNA double strand break repair: signaling and single-stranded resection dictate the choice between homologous recombination, non-homologous end-joining and alternative end-joining

Affiliations

Initiation of DNA double strand break repair: signaling and single-stranded resection dictate the choice between homologous recombination, non-homologous end-joining and alternative end-joining

Anastazja Grabarz et al. Am J Cancer Res. 2012.

Abstract

A DNA double strand break (DSB) is a highly toxic lesion, which can generate genetic instability and profound genome rearrangements. However, DSBs are required to generate diversity during physiological processes such as meiosis or the establishment of the immune repertoire. Thus, the precise regulation of a complex network of processes is necessary for the maintenance of genomic stability, allowing genetic diversity but protecting against genetic instability and its consequences on oncogenesis. Two main strategies are employed for DSB repair: homologous recombination (HR) and non-homologous end-joining (NHEJ). HR is initiated by single-stranded DNA (ssDNA) resection and requires sequence homology with an intact partner, while NHEJ requires neither resection at initiation nor a homologous partner. Thus, resection is an pivotal step at DSB repair initiation, driving the choice of the DSB repair pathway employed. However, an alternative end-joining (A-EJ) pathway, which is highly mutagenic, has recently been described; A-EJ is initiated by ssDNA resection but does not require a homologous partner. The choice of the appropriate DSB repair system, for instance according the cell cycle stage, is essential for genome stability maintenance. In this context, controlling the initial events of DSB repair is thus an essential step that may be irreversible, and the wrong decision should lead to dramatic consequences. Here, we first present the main DSB repair mechanisms and then discuss the importance of the choice of the appropriate DSB repair pathway according to the cell cycle phase. In a third section, we present the early steps of DSB repair i.e., DSB signaling, chromatin remodeling, and the regulation of ssDNA resection. In the last part, we discuss the competition between the different DSB repair mechanisms. Finally, we conclude with the importance of the fine tuning of this network for genome stability maintenance and for tumor protection in fine.

Keywords: DNA double strand break; Homologous recombination; Non homologous end joining; Resection; alternative end-joining; chromatin remodeling; genetic instability; genome rearrangements.

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Figures

Figure 1
Figure 1
A) The double-strand break repair model. Resection of ssDNA generates single-stranded 3’tails that can invade a homologous double-stranded DNA, forming a D-loop (displacement loop). Synthesis of DNA is primed from the 3’end of the invasive strand. The D-loop can hybridize with the second single-stranded 3’end. DNA synthesis repairs the break and can therefore fill gaps. Cruciform junctions called Holliday junctions are formed and can migrate. Resolution of these junctions can occur in two different orientations (black or grey triangles) resulting in either gene conversion associated with crossing over or gene conversion without crossing over. B) Synthesis-dependent strand annealing (SDSA). Initiation is similar to that of the previous model, with a single-strand resection, invasion of the homologous double-stranded DNA and DNA synthesis, but the invading strand dehybridizes and reanneals at the other end of the injured molecule; no Holliday junction is thus formed. This model only accounts for gene conversion without crossovers. C) Break-induced replication (BIR). Initiation is similar to that of the previous models, with a single-strand resection, invasion of the homologous double-stranded DNA and DNA synthesis, but the synthesis continues over longer distances on the chromosome arms and even can reach the end of the chromosome. Here again, there is neither resolution of Holliday junctions nor crossover. D) Single-strand annealing (SSA). A double-strand break occurs between two homologous sequences in tandem in the same orientation (dotted arrows) (a). A single-strand resection then reveals two complementary DNA strands that can hybridize (b). If the tandem sequences are in opposite orientations, the revealed single strands of DNA are not complementary but are identical; they therefore cannot hybridize. In this process, the break does not need to be in or near a region of homology. (c) Resolution of this intermediate and filling the gap of the single strand completes the repair of the double-strand break, leading to the deletion of the intergenic sequences between the initial repetitions.
Figure 2
Figure 2
A. The different stages of canonical NHEJ and AE-J. After the formation of DSBs, the heterodimer Ku70/Ku80 interacts with the ends of the damaged DNA and promotes the recruitment of DNA-PKcs and Artemis. Artemis processes the ends of the DNA to make them compatible for enzymatic ligation by the complex Cernunnos-XLF/XRCC4/Ligase IV complex at the final step. B/ A-EJ: Alternatively, DNA ends that are not protected by Ku70/Ku80 are degraded. It is proposed that a single strand DNA resection reveals complementary microhomologies (2 to 4 nt and more), which can anneal; filling in of the single strand gap or nick complete the end-joining. A-EJ (for Alternative end-joining) is always mutagenic, with deletion at the junctions and frequently (but not systematically) uses microhomologie distant from the DSB. A-EJ is independent on Ku80, Xrcc4, Ligase IV, and is dependent on Parp1, Ligase III. The nuclease activity of MRE11 favors A-EJ.
Figure 3
Figure 3
Model for sequential steps for DSB repair. The MRN complex is involved at early step of DSB signaling and can activate both C-NHEJ and A-EJ. Binding of Ku80/Ku70 and C-NHEJ protects from ssDNA resection leading to a conservative DSB repair outcome. Short ssDNA resection allows A-EJ but not homologous recombination. Long ssDNA resection allows A-EJ, but homologous recombination requires the activation of the subsequent steps such as the loading of RAD51 on the ssDNA.
Figure 4
Figure 4
A) Chromosomal rearrangements resulting from crossovers (CO). (1) CO between repetitions on two chromosomes or unequal sister chromatids exchange results in amplification of one molecule and deletion of the other. (2) Intra-chromosomal CO between two direct repeat sequence, results in excision of the intervening sequence. (3) CO between two inverted repeat sequences leads to inversion of the internal fragment. (4) and (5) Inter-chromosomal CO. According to the orientation of the sequences with respect to the centromers (black or grey circles), the process generates a translocation (4) or one dicentric and one acentric chromosome (5). B) Genetic modifications resulting from gene conversion between two heteroalleles, leading to a loss of heterozygosity (upper panel). Lower panel: Gene conversion between one pseudogene (hatched), which often contains nonsense mutations (black bar), and one gene, leading to the inactivation of the latter.
Figure 5
Figure 5
A/ I/ A replication fork reaching a single-stranded gap in the template, results in a collapsed fork. Recombination with the sister chromatid allows the restarting of the fork via a process similar to BIR (see Figure 1). II/ (1) When the fork reaches a blocking lesion (grey scare), fork reversion forms a structure called “chicken foot” (2); (3) the cruciform structure can be resolved (in the manner of a Holliday junction), resulting in a double end (4). Note that in both case single double strand ends are generated, a situation different from DSB induced by endonucleases or IR in which two close double strand ends are generated, favoring end-joining. B) Recombination with the sister chromatid (Left panel) allows replication to restart by a BIR-like mechanism, maintaining genome stability. In such situation, NHEJ, which join distant single-ended double strand ends, resulting thus in genetic exchange (Right panel).
Figure 6
Figure 6
Chromatin remodelling in response to DSBs. H2AX (phosphoryltaion by ATM) and histone H3 (acetylation by GCN5) are modified at low levels on DSB flanking regions. This helps the recruitment of MDC1. GCN5 then binds to firstly phosphorylated H2AX, which increases histones acetylation and facilitates the recruitment of SWI/SNF chromatin remodelling factors. They increase the accessibility of chromatin to chromatin remodelling and repair factors. Sin3 and MOF1 acetylate histone H4, which also helps the efficient recruitment of MDC1, BRCA1 and 53BP1. MDC1 recruit RNF8 and RNF168 that mediate the ubiquitylation of histones. RAP80, through its ubiquitin-binding domain, recruits BRCA1 and the other members of the ABRAXAS complex at DSBs. These reactions are amplified upon the chromatin relaxation operated by NuA4, Tip60, Ino80, CHD4 and P400. MDC1 also recruits MMSET and SET8 methyltransferases that methylate histone H4. This, with histones ubiquitylation mediated by RNF8 and RNF168, mediates the chromatin relaxation by EXPAND.

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