Meiotic recombination hotspots: shaping the genome and insights into hypervariable minisatellite DNA change

Abstract

Meiotic homologous recombination serves three principal roles. First, recombination reassorts the linkages between newly-arising alleles to provide genetic diversity upon which natural selection can act. Second, recombination is used to repair certain types of DNA damage to provide a mechanism of genomic homeostasis. Third, with few exceptions homologous recombination is required for the appropriate segregation of homologous chromosomes during meiosis. Recombination rates are elevated near DNA sites called "recombination hotspots." These sites influence the distribution of recombination along chromosomes and the timing of recombination during the life cycle. Recent advances have revealed biochemical steps of hotspot activation and have suggested that hotspots may regulate when and where recombination occurs. Two models for hotspot activation, one in which hotspots act early in the recombination pathway and one in which hotspots act late in the recombination pathway, are presented. The latter model can account for changes at hypervariable minisatellite DNA in metazoan genomes by invoking resolution of Holliday junctions at minisatellite DNA repeats.

Figure 1. Schematic diagram of differences between physical and meiotic genetic maps

Expansion and contraction of genetic intervals relative to physical intervals identifies regions of the genome with rates of recombination higher (interval 1) and lower (interval 3) than average, respectively. In this idealized example recombination is higher in interval 1 during male meiosis relative to female meiosis, revealing sex-specific differences of recombination rates. Cis-acting elements within or nearby the intervals are inferred to influence their rates of recombination.

Figure 2. Polarity of recombination

(A) Reciprocal exchange is conservative and switches the linkage between markers flanking the point of recombination. Gene conversion and postmeiotic segregation (PMS) are nonconservative (aberrant) recombination events that result from the transfer of the genetic information from one allele to the other. Other types of aberrant segregation (not shown) may also occur Aberrant segregation events in unselected tetrads can be used to gauge recombination rates at individual genetic markers. (B) An example of polarity resulting from different frequencies of aberrant segregation for multiple markers at the DED81 and ARG4 loci in S. cerevisiae. Regions of increased accessibility of DNA within meiotic chromatin (striped balloons) and meiosis-specific dsDNA breaks (DSB arrows) map to the high-frequency end of polarity gradients, suggesting that recombination initiates at those sites. Data are from (Fogel et al., 1981; White et al., 1985; Nicolas et al., 1989; Sun et al., 1989; Cao et al., 1990; Schultes and Szostak, 1990; Lichten, 1995).

Figure 3. A dsDNA break repair model of recombination

1. Mitotic chromosomes with associated DNA binding proteins (balloons). 2. During meiosis, the binding proteins are altered by post-translational modification or by interaction with meiotic factors to generate chromatin in which the DNA becomes more accessible. 3. Spo11 protein (filled circle) assembles at the site, either via protein-protein interactions or by recognizing an altered chromatin conformation at the hotspot. 4. A topoisomerase II-like, dsDNA cleavage reaction by Spo11 protein produces covalent protein-DNA intermediates with phosphodiester linkages between active site tyrosines and the 5′ terminal phosphate groups of the broken strands. 5. Release of protein is achieved by hydrolysis of the phosphotyrosine linkage or by nucleolytic cleavage of the covalently-bound strand (step 5′). Exonucleolytic resection (dotted line) generates free, 3′ ssDNA tails which can invade the homologous dsDNA to produce heteroduplex DNA. 6. The invading strand is extended by DNA synthesis (arrow) to produce a displacement loop. 7. Annealing of the remaining free 3′ strand to the displacement loop and further DNA synthesis fills the existing gaps. 8. Ligation of DNA strands results in chromosomes attached by two Holliday junctions. Branch migration of the junctions may occur (not shown). The junctions are resolved by cleavage of two DNA strands. Depending upon which strands are cleaved, the resulting chromosomes either lack reciprocal exchange of flanking markers (step 9) or have reciprocal exchange (step 9′). Additional details and references are provided in the text.

Figure 4. A model for recombination hotspot activity and formation of polarized variability at hypervariable minisatellite DNA

(A) Schematic representation of polarized variability. Individual minisatellite repeats (boxes) can be sometimes be distinguished by minor sequence differences within each repeat (black or white). Arising alleles are uniform across most of the locus and then become mosaic towards one end of the locus. (B) Model for recombination hotspot activity and generation of polarized variability. 1. Initiating event leads to strand exchange and generation of a Holliday junction. 2. Branch migration of the Holliday junction. 3. An element within each minisatellite DNA repeat provides the signal to resolve the Holliday junction. Resolution can occur by the major pathway (nick strands at horizontal arrows) or by the minor pathway (nick strands at vertical arrows). 4. Resolution by the major pathway yields recombinants with heteroduplex DNA and no reciprocal exchange of flanking markers. 5. Short patch mismatch repair (up and down arrows) acts independently on each repeat to generate polarized variability. Loci with incomplete mismatch repair will exhibit postmeiotic segregation (not shown). 4′. Resolution by the minor pathway yields recombinants with heteroduplex DNA and reciprocal exchange of flanking markers. 5′. Short patch mismatch repair of the minor product also generates polarized variability. Additional details and references are provided in the text.