Protein Determinants of Meiotic DNA Break Hot Spots.
ABSTRACT Meiotic recombination, crucial for proper chromosome segregation and genome evolution, is initiated by programmed DNA double-strand breaks (DSBs) in yeasts and likely all sexually reproducing species. In fission yeast, DSBs occur up to hundreds of times more frequently at special sites, called hot spots, than in other regions of the genome. What distinguishes hot spots from cold regions is an unsolved problem, although transcription factors determine some hot spots. We report the discovery that three coiled-coil proteins-Rec25, Rec27, and Mug20-bind essentially all hot spots with great specificity even without DSB formation. These small proteins are components of linear elements, are related to synaptonemal complex proteins, and are essential for nearly all DSBs at most hot spots. Our results indicate these hot spot determinants activate or stabilize the DSB-forming protein Rec12 (Spo11 homolog) rather than promote its binding to hot spots. We propose a paradigm for hot spot determination and crossover control by linear element proteins.
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ABSTRACT: Although the standard laboratory strain of S. pombe has been extensively studied, genetic variation and phenotypic diversity have been analyzed only in preliminary ways 1–3. Remarkably little is known about the evolutionary history or ecology of this model organism. It was first described in East African millet beer in 1893, and the standard laboratory strain was isolated from French wine in 1924 (ref. 4). Natural isolates have also been collected from vineyards in Sicily and cachaça (a sugarcane spirit) in Brazil and have been found to contribute to the microbial ecology of kombucha (fermented tea) 1,5,6. The diverse origins of these natural isolates (Fig. 1a and Supplementary Table 1) suggest that this yeast species is now widely distributed. To further describe S. pombe, we analyzed the genetic and phenotypic variation in natural isolates. Because the natural environment is not known, we collected all isolates available from the major stock centers and those given to us by microbial ecologists (Supplementary Table 1). These 161 strains had been collected over the last 100 years, in over 20 countries across the globe, primarily from cultivated fruit or various fermentations. Notably, the strains of known origin had been associated with human activities, providing little information about the natural environment of the species. RESULTS Variation and population structure We sequenced the genome of all strains to at least 18-fold coverage , with a median of 76-fold coverage. To facilitate the detection of genetic variants, we mapped reads to the reference genome 7. Mapping was comprehensive and accurate owing to the small, non-repetitiveNature Genetics 02/2015; 2015/02/09/online. DOI:10.1038/ng.3215 · 29.65 Impact Factor
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ABSTRACT: BackgroundG-quadruplexes (G4s) are stable non-canonical DNA secondary structures consisting of stacked arrays of four guanines, each held together by Hoogsteen hydrogen bonds. Sequences with the ability to form these structures in vitro, G4 motifs, are found throughout bacterial and eukaryotic genomes. The budding yeast Pif1 DNA helicase, as well as several bacterial Pif1 family helicases, unwind G4 structures robustly in vitro and suppress G4-induced DNA damage in S. cerevisiae in vivo.ResultsWe determined the genomic distribution and evolutionary conservation of G4 motifs in four fission yeast species and investigated the relationship between G4 motifs and Pfh1, the sole S. pombe Pif1 family helicase. Using chromatin immunoprecipitation combined with deep sequencing, we found that many G4 motifs in the S. pombe genome were associated with Pfh1. Cells depleted of Pfh1 had increased fork pausing and DNA damage near G4 motifs, as indicated by high DNA polymerase occupancy and phosphorylated histone H2A, respectively. In general, G4 motifs were underrepresented in genes. However, Pfh1-associated G4 motifs were located on the transcribed strand of highly transcribed genes significantly more often than expected, suggesting that Pfh1 has a function in replication or transcription at these sites.Conclusions In the absence of functional Pfh1, unresolved G4 structures cause fork pausing and DNA damage of the sort associated with human tumors.BMC Biology 12/2014; 12(1):101. DOI:10.1186/s12915-014-0101-5 · 7.43 Impact Factor
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ABSTRACT: Meiotic recombination involves the formation and repair of programmed DNA double-strand breaks (DSBs) catalyzed by the conserved Spo11 protein. This review summarizes recent studies pertaining to the formation of meiotic DSBs, including the mechanism of DNA cleavage by Spo11, proteins required for break formation, and mechanisms that control the location, timing, and number of DSBs. Where appropriate, findings in different organisms are discussed to highlight evolutionary conservation or divergence.Cold Spring Harbor perspectives in biology 10/2014; 7(1). DOI:10.1101/cshperspect.a016634 · 8.23 Impact Factor