Novel Nucleotide Sequence Motifs That Produce Hotspots of Meiotic Recombination inSchizosaccharomyces pombe

Abstract

In many organisms, including yeasts and humans, meiotic recombination is initiated preferentially at a limited number of sites in the genome referred to as recombination hotspots. Predicting precisely the location of most hotspots has remained elusive. In this study, we tested the hypothesis that hotspots can result from multiple different sequence motifs. We devised a method to rapidly screen many short random oligonucleotide sequences for hotspot activity in the fission yeast Schizosaccharomyces pombe and produced a library of $500 unique 15-and 30-bp sequences containing hotspots. The frequency of hotspots found suggests that there may be a relatively large number of different sequence motifs that produce hotspots. Within our sequence library, we found many shorter 6-to 10-bp motifs that occurred multiple times, many of which produced hotspots when reconstructed in vivo. On the basis of sequence similarity, we were able to group those hotspots into five different sequence families. At least one of the novel hotspots we found appears to be a target for a transcription factor, as it requires that factor for its hotspot activity. We propose that many hotspots in S. pombe, and perhaps other organisms, result from simple sequence motifs, some of which are identified here.

Important Characteristics of Sequence-Specific Recombination Hotspots in Schizosaccharomyces pombe

“…Strains were constructed by linear transformation of WS129, which contains a ura4 1 -kanMX6 construct inserted in the ade6 gene (Steiner et al 2009). …”

“…Transformation was performed using lithium acetate as previously described (Steiner et al 2009). All transformants were verified by sequencing and Southern blot hybridization.…”

“…Each of the homothallic strains shown in Table 1 contains the plasmid pWS35, which carries a 613-bp fragment of the ade6 gene (Steiner et al 2009). Thus, the chromosomal copy of ade6 can recombine with the plasmid to become ade6 1 during meiosis.…”

“…In S. pombe, we identified a large number of unique sequences that create meiotic recombination hotspots (Steiner et al 2009). Many of these sequences contained common motifs that could be grouped into five distinct families, including the previously identified CRE family of hotspots (Fox et al 2000).…”

Is the control of recombination conserved among diverse eukaryotes?

“…The zinc-finger domains of human PRDM9 bind preferentially to a minority (B40%) of such hotspots through a degenerate 13-bp consensus motif (Myers et al, 2008). Hotspots are also evident in yeast, with one or more of five classes of degenerate DNA sequence motifs being present in 60% of randomly generated DSB hotspots for Schizosaccharomyces pombe (Steiner et al, 2009). Across the eukaryotic lineage, meiotic DNA cleavage activity is catalysed by orthologous Spo11 enzymes, thereby placing a conserved enzymatic activity at the heart of this fundamental cellular process.…”