A Discrete Class of Intergenic DNA Dictates Meiotic DNA Break Hotspots in Fission Yeast

Abstract

Meiotic recombination is initiated by DNA double-strand breaks (DSBs) made by Spo11 (Rec12 in fission yeast), which becomes covalently linked to the DSB ends. Like recombination events, DSBs occur at hotspots in the genome, but the genetic factors responsible for most hotspots have remained elusive. Here we describe in fission yeast the genome-wide distribution of meiosis-specific Rec12-DNA linkages, which closely parallel DSBs measured by conventional Southern blot hybridization. Prominent DSB hotspots are located ∼65 kb apart, separated by intervals with little or no detectable breakage. Most hotspots lie within exceptionally large intergenic regions. Thus, the chromosomal architecture responsible for hotspots in fission yeast is markedly different from that of budding yeast, in which DSB hotspots are much more closely spaced and, in many regions of the genome, occur at each promoter. Our analysis in fission yeast reveals a clearly identifiable chromosomal feature that can predict the majority of recombination hotspots across a whole genome and provides a basis for searching for the chromosomal features that dictate hotspots of meiotic recombination in other organisms, including humans. Homologous genetic recombination has two immediate benefits for cells—faithfully repairing broken DNA and aiding chromosome segregation during the first division of meiosis. Meiosis comprises a pair of special nuclear divisions that convert diploid somatic cells into haploid sex cells; in humans, meiosis leads to formation of eggs and sperm. By introducing double-strand breaks (DSBs) into their own DNA during meiosis, organisms promote recombination and hence production of viable sex cells. Although meiotic DSBs, and therefore recombination, occur throughout genomes, they arise at high frequency in certain genomic regions called hotspots, whose molecular bases are rarely understood. In this article we determine the locations of DSBs across the entire genome of the fission yeast Schizosaccharomyces pombe by taking advantage of physical linkages between DNA and the protein Rec12 that makes DSBs. This analysis shows that most of the DSB hotspots are in exceptionally large intergenic (gene-free) regions spaced on average about 65 kb apart and making up only a small fraction of the genome. Between the hotspots we see very little evidence of DSBs. The concentration of hotspots in large intergenic regions suggests that DSBs may be determined by special nucleotide sequences buried in these regions. Determining these special sequences will allow predictions of hotspots and, perhaps, the proteins and features of genome architecture that lead to DSBs being made at these special sites.