Natural Meiotic Recombination Hot Spots in the Schizosaccharomyces pombe Genome Successfully Predicted from the Simple Sequence Motif M26

Abstract

The M26 hot spot of meiotic recombination in Schizosaccharomyces pombe is the eukaryotic hot spot most thoroughly investigated at the nucleotide level. The minimum sequence required for M26 activity was previously determined to be 5-ATGACGT-3. Originally identified by a mutant allele, ade6-M26, the M26 heptamer sequence occurs in the wild-type S. pombe genome approximately 300 times, but it has been unclear whether any of these are active hot spots. Recently, we showed that the M26 heptamer forms part of a larger consensus sequence, which is significantly more active than the heptamer alone. We used this expanded sequence as a guide to identify a smaller number of sites most likely to be active hot spots. Ten of the 15 sites tested showed meiotic DNA breaks, a hallmark of recombination hot spots, within 1 kb of the M26 sequence. Among those 10 sites, one occurred within a gene, cds1؉ , and hot spot activity of this site was confirmed genetically. These results are, to our knowledge, the first demonstration in any organism of a simple, defined nucleotide sequence accurately predicting the locations of natural meiotic recombination hot spots. M26 may be the first example among a diverse group of simple sequences that determine the distribution, and hence predictability, of meiotic recombination hot spots in eukaryotic genomes.Homologous recombination occurs at high frequency during meiosis in most sexually reproducing organisms (4). Crossovers resulting from recombination create connections between homologous chromosomes (chiasmata), which are critical for the proper segregation of chromosomes at the first meiotic division. In the absence of recombination, homologs segregate nearly randomly in most organisms, often resulting in aneuploid meiotic products (gametes or spores). Aneuploid progeny in multicellular eukaryotes, such as humans, are usually inviable or suffer from a number of physical and mental abnormalities, as seen, for example, in human trisomy 21 (Down syndrome). In addition to its role in the proper segregation of chromosomes, meiotic recombination also results in the formation of new genetic combinations and is therefore an important mechanism of increasing genetic diversity within a species.Recombination does not occur at a uniform frequency throughout the genomes of the organisms examined. Rather, there are sites that recombine at a significantly higher or lower frequency than the genomic average, termed hot spots and cold spots, respectively. Hot spots have been described in organisms as diverse as bacteria and their phages, mice, and humans (9, 26, 30). In the two distantly related yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, meiotic hot spots of recombination are sites of programmed double-strand DNA breaks (DSBs) made by the Spo11 protein (Rec12 in S. pombe) (11,26,31,33). Spo11 is a meiotically induced protein with amino acid sequence similarity to an archaeal type II topoisomerase, TopoVI. Spo11 homologs are widely conserved in eukaryotes and are essential for meiotic recom...

Nucleosomal organization of replication origins and meiotic recombination hotspots in fission yeast

“…Given this preference, we wondered whether ORIs and DSBs might tend to share the same IGRs. To address this issue experimentally, we tested ORI activity during the meiotic Sphase in 13 genomic loci previously found to generate DSBs (Cromie et al, 2005;Steiner and Smith 2005) (Figure 1A). Analysis of replication intermediates by two-dimensional gel electrophoresis revealed that 8 out of 13 (60%) DSB regions colocalized with active meiotic ORIs ( Figure 1B, see Figure 3B for mbs1 analysis).…”

“…Further examples of DSBs regions ranging from a few hundred nucleotides up to over 2 kb have been reported by Steiner and Smith (2005) and by Cromie et al (2007). An expanded consensus of the M26 sequence has been used successfully to predict the localization of some DSBs, although not all regions harbouring the consensus generate DSBs and most genomic DSBs do not include it (Steiner and Smith, 2005;Cromie et al, 2007). A similar situation applies to other recombination hotspots associated with specific sequences such as HIS4 in S. cerevisiae (White et al, 1993;Mieczkowski et al, 2006) and a degenerate C-rich motif in humans (Myers et al, 2008).…”

“…The use of sequence motifs as predictors of DSBs in S. pombe (Steiner and Smith, 2005), S. cerevisiae (Mieczkowski et al, 2006) and humans (Myers et al, 2008) has usually generated a significant fraction of false positives, indicating that additional chromatin or epigenetic elements are also needed. Our results and those of Pan et al (2011) in S. cerevisiae suggest that NDRs are an obligatory requirement in the specification of DSBs, such that the incorporation of this feature could improve sequence-based predictions.…”

A population genetics model with recombination hotspots that are heterogeneous across the population

“…In humans, researchers have measured gene conversion tract lengths averaging less than this distance, namely several hundred base pairs (26). In prokaryotes (27, 28) and yeast (24,29), such hotspot-causing motifs have been identified. In humans, there is compelling evidence that some hotspot-causing motifs are found in retrotransposons; however, these motifs explain Ͻ20% of the inferred human hotspots (2, 30-32).…”

“…Researchers have considered positive selection on the hotspot or multiple hotspots at different nearby positions, without successfully resolving the paradox (22,23). Another suggestion (24) is that perhaps there is some distance between the motif and the break position: after a break event, then, whether or not the motif is transmitted depends on this distance and the amount of lost DNA. In yeast, researchers have observed double-strand breaks as far as 1.3 kb away from a known motif (25).…”