ysical 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.
Citation: Cromie GA, Hyppa RW, Cam HP, Farah JA, Grewal SIS, Smith GR (2007) A Discrete Class of Intergenic DNA Dictates Meiotic DNA Break Hotspots in Fission Yeast. PLoS Genet 3(8): e141. doi:10.1371/journal.pgen.0030141
Editor: James E. Haber, Brandeis University, United States of America
Received: May 10, 2007; Accepted: July 9, 2007; Published: August 24, 2007
This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
Funding: This research was supported by research grant GM031693 from the National Institutes of Health of the United States of America to GRS, and institutional funds from the Fred Hutchinson Cancer Research Center to GRS and from the National Cancer Institute to SISG.
Competing interests: The authors have declared that no competing interests exist.
Abbreviations: DSB, double-strand break; GC, guanine-cytosine; GO, gene ontology; IGR, intergenic region; IP, immunoprecipitate; WCE, whole cell extract
Genome-wide analysis of a molecular event can provide insights, such as identification of patterns within the data at multiple scales, which are unavailable through study of single events. Using the fission yeast Schizosaccharomyces pombe, we analyze an event, the formation of DNA double-strand breaks (DSBs), which is essential for meiotic recombination. We find that hotspots of DSB formation occur primarily in unusually large intergenic regions (IGRs) and are widely separated by apparently break-free regions. Our results show that a clearly identifiable subset of noncoding DNA has a special function that is critical for meiosis. These results contrast with those obtained in the distantly related budding yeast Saccharomyces cerevisiae.
Meiosis consists of two special nuclear divisions during which chromosome number is reduced from two in somatic cells to one in gametes. Uniquely, in the first meiotic division homologs, rather than sister chromatids, segregate from each other. In most organisms homolog segregation is aided by crossover recombination.
Meiotic recombination is initiated by DSBs in both budding and fission yeasts and perhaps in all species [1–3]. Repair of the DSBs by interaction with a homolog produces the crossovers (reciprocal recombination events) important for homolog segregation and for the generation of genetic diversity. DSBs are formed by a meiosis-specific protein Spo11 (Rec12 in S. pombe) through a topoisomerase-like mechanism, in which a tyrosine residue of the protein forms a phosphodiester covalent linkage with each 5′ end at the DSB [3,4]. DSBs can be detected by extraction of DNA from meiotic cells and analyzing it by Southern blot hybridizations, which reveal distinct hotspots of break formation. DSBs are transient in wild-type cells but accumulate to high levels in mutants, such as rad50S, in which the Spo11 or Rec12 protein is not removed from the ends of breaks [2,5]. Analysis of DSBs is thus more sensitive in rad50S cells.
DSB hotspots were first detected at recombination hotspots, sites at which gene conversion (nonreciprocal recombination) occurs at especially high frequency. Gene conversion hotspots have been identified in the wild-type chromosomes of many species, including humans, and 