Genome destabilization by homologous recombination in the germ line

Abstract

Meiotic recombination, which promotes proper homologous chromosome segregation at the first meiotic division, normally occurs between allelic sequences on homologues. However, recombination can also take place between non-allelic DNA segments that share high sequence identity. Such non-allelic homologous recombination (NAHR) can markedly alter genome architecture during gametogenesis by generating chromosomal rearrangements. Indeed, NAHR-mediated deletions, duplications, inversions and other alterations have been implicated in numerous human genetic disorders. Studies in yeast have provided insights into the molecular mechanisms of meiotic NAHR as well as the cellular strategies that limit it.

Figure 1. Meiotic recombination pathway

A double-strand break (DSB) introduced by Spo11 is resected to expose 3′ ssDNA tails. Mediated by Rad51 and Dmc1, one of the 3′ ssDNA tails first invades the homologous chromosome to form a displacement loop (D-loop) and heteroduplex DNA (highlighted), and then initiates DNA synthesis. In the canonical pathway, capture of the second end, DNA synthesis and ligation generate Holliday junctions flanking the DSB site. The Holliday junctions can be resolved by cutting the outside strands (filled arrowheads) or crossed strands (open arrowheads) of each junction (two of the four possible resolution configurations are shown here). In principle, resolution can lead to either a crossover or a noncrossover configuration of the DNA flanking the recombination site. In vivo, however, most resolution products are crossovers. An alternative recombination pathway depicted on the right (known as synthesis-dependent strand annealing (SDSA)) leads primarily to noncrossovers. In both types of pathway, gene conversion can occur by mismatch repair if DNA sequence polymorphisms are incorporated into the heteroduplex DNA that forms as part of the recombination process.

Figure 2. Genome rearrangement by non-allelic homologous recombination

Crossover recombination between repeated DNA sequences at non-allelic positions can generate a deletion, a duplication, an inversion or an isodicentric chromosome. Depicted here are six chromosomal outcomes of non-allelic homologous recombination (NAHR) between repeats located on the same chromosome: two orientations of repeats relative to one another (direct or inverted) for each of three types of interactions (between homologues, between sister chromatids or in the same chromatid). Homologous chromosomes are shown in blue and red, and sister chromatids are depicted in the same colour (homologous chromosomes are not shown in the schematics depicting inter-sister chromatid or intrachromatid exchanges for simplicity). Low-copy repeats (LCRs) are shown as white and black arrowheads. Figure modified, with permission, from REF. 55.

Figure 3. Non-allelic homologous recombination between artificially duplicated repeats in yeast

a | Non-allelic homologous recombination (NAHR) between interstitial repeats. Artificial repeats (depicted as arrowheads) located interstitially in allelic positions (a) and artificial repeats in non-allelic positions (b) on homologous chromosomes (blue and red) recombine with similar efficiency. By contrast, repeats located on heterologous chromosomes (blue and yellow) recombine ~10-fold less efficiently (c) than allelic sequences. These findings suggest that, compared with repeats on heterologues, repeats on homologues are in a closer proximity, probably through recombination-dependent homologue pairing. b | NAHR between subtelomeric repeats. An artificial repeat located in a subtelomeric region recombines only slightly less efficiently with another subtelomeric repeat (two-six fold less than between allelic repeats on homologues (a)), whether on the opposite chromosome arm (b) of the homologue or on a heterologue (c). The dynamic organization of telomeres during prophase of the first meiotic division (that is, attachment to the nuclear envelope and bouquet formation) might increase the proximity of telomeric regions of different chromosomes and thus influence the frequency of NAHR.

Figure 4. The influence of homologue pairing on recombination

a | Double-strand break (DSB)-dependent homologue pairing in budding yeast. After pre-meiotic DNA replication, homologous chromosomes are dispersed in the nucleus. DSBs are formed early in meiotic prophase, providing substrates for recombination proteins to carry out homology search and strand invasion, and resulting in the alignment of homologous chromosome axes at multiple sites (axial interactions). As recombination continues, homologue interactions are progressively stabilized, culminating in the formation of the synaptonemal complex. The development of progressively more stable pairing interactions may inhibit non-allelic homologous recombination (NAHR) by juxtaposing allelic sequences in close proximity. b | The influence of homologue pairing on restraining NAHR. Under normal homologue pairing conditions, NAHR between artificial repeats (indicated by arrowheads) located on one of the paired homologues and on a heterologue occurs at a low level. When pairing between the homologues is disrupted because of sequence divergence between them, the frequency of NAHR between the artificial repeats on heterologues increases ~seven-fold. c | Persistence of recombinational DSBs in unpaired regions of the genome. Mouse chromosomes with semi-identical reciprocal translocations (shown schematically in right pamel) undergo homologous pairing and synapsis along most of their lengths and DSBs are repaired in synapsed regions (left panel), However, DSBs in sequences that are not shared between homologues persist into pachytene despite the presence of identical sequences on heterologues.

Figure 5. Suppression of recombination between divergent sequences

When a double-strand [see cover letter comment 1] break (DSB) undergoes strand invasion, heteroduplex DNA is formed. When there are few or no mismatched bases, subsequent recombination processes continue. However, when there are many mismatches, mismatch repair (MMR) proteins (such as Pms1 and Msh2) impede strand invasion steps that could lead to crossover formation. Subsequently, heteroduplex DNA might be destabilized (known as heteroduplex rejection) and possibly channelled into the synthesis-dependent strand annealing (SDSA) pathway, which leads to a noncrossover outcome.