Genome-Wide Detection of Polymorphisms at Nucleotide Resolution with a Single DNA Microarray

Gresham, David; Ruderfer, Douglas M.; Pratt, Stephen C.; Schacherer, Joseph; Dunham, Maitreya J.; Botstein, David; Kruglyak, Leonid

doi:10.1126/science.1123726

Cited by 236 publications

(238 citation statements)

References 29 publications

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“…Complementation tests revealed that these mutants do not complement each other, implicating a single locus. One of the mutants, DBY11202, was used for both array-assisted bulk segregant analysis (14) and mutation detection by using overlapping tiling arrays of the entire yeast genome (15). The bulk segregant analysis identified one linkage peak on chromosome IV (Fig.…”

Section: Resultsmentioning

confidence: 99%

Influence of genotype and nutrition on survival and metabolism of starving yeast

Boer

Amini

Botstein

2008

Proc. Natl. Acad. Sci. U.S.A.

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124

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Starvation of yeast cultures limited by auxotrophic requirements results in glucose wasting and failure to achieve prompt cell-cycle arrest when compared with starvation for basic natural nutrients like phosphate or sulfate. We measured the survival of yeast auxotrophs upon starvation for different nutrients and found substantial differences: When deprived of leucine or uracil, viability declined exponentially with a half-life of <2 days, whereas when the same strains were deprived of phosphate or sulfate, the half-life was Ϸ10 days. The survival rates of nongrowing auxotrophs deprived of uracil or leucine depended on the carbon source available during starvation, but were independent of the carbon source during prior growth. We performed an enrichment procedure for mutants that suppress lethality during auxotrophy starvation. We repeatedly found loss-of-function mutations in a number of functionally related genes. Mutations in PPM1, which methylates protein phosphatase 2A, and target of rapamycin (TOR1) were characterized further. Deletion of PPM1 almost completely suppressed the rapid lethality and substantially suppressed glucose wasting during starvation for leucine or uracil. Suppression by a deletion of TOR1 was less complete. We suggest that, similar to the Warburg effect observed in tumor cells, starving yeast auxotrophs wastes glucose as a consequence of the failure of conserved growth control pathways. Furthermore, we suggest that our results on condition-dependent chronological lifespan have important implications for the interpretation and design of studies on chronological aging. auxotrophy starvation ͉ chronological aging ͉ Warburg effect

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Section: Resultsmentioning

confidence: 99%

Influence of genotype and nutrition on survival and metabolism of starving yeast

Boer

Amini

Botstein

2008

Proc. Natl. Acad. Sci. U.S.A.

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124

183

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“…Improvements will come especially from better estimates of the mutation rate, the recombination rate and its heterogeneity along the chromosome, and the inbreeding coefficient. Modern genomic technologies make such improvements increasingly possible (40)(41)(42), potentially allowing us to learn almost as much about the reproductive habits of microbes like yeast as can be learned from direct observation of large organisms such as plants and animals. …”

Section: Discussionmentioning

confidence: 99%

Population genomics of the wild yeast Saccharomyces paradoxus : Quantifying the life cycle

Tsai

Bensasson

Burt

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

296

321

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Most microbes have complex life cycles with multiple modes of reproduction that differ in their effects on DNA sequence variation. Population genomic analyses can therefore be used to estimate the relative frequencies of these different modes in nature. The life cycle of the wild yeast Saccharomyces paradoxus is complex, including clonal reproduction, outcrossing, and two different modes of inbreeding. To quantify these different aspects we analyzed DNA sequence variation in the third chromosome among 20 isolates from two populations. Measures of mutational and recombinational diversity were used to make two independent estimates of the population size. In an obligately sexual population these values should be approximately equal. Instead there is a discrepancy of about three orders of magnitude between our two estimates of population size, indicating that S. paradoxus goes through a sexual cycle approximately once in every 1,000 asexual generations. Chromosome III also contains the mating type locus (MAT), which is the most outbred part in the entire genome, and by comparing recombinational diversity as a function of distance from MAT we estimate the frequency of matings to be Ϸ94% from within the same tetrad, 5% with a clonemate after switching the mating type, and 1% outcrossed. Our study illustrates the utility of population genomic data in quantifying life cycles. mating systems ͉ inbreeding ͉ sex ͉ nucleotide polymorphism ͉ linkage disequilibrium M icrobial life cycles are often difficult to study because the organisms involved are so small. Laboratory studies can reveal what a species is capable of doing, but give little information on the frequencies of different modes of reproduction in nature. Instead, we must look at patterns of DNA sequence variation to infer the reproductive system. Pioneered by studies in bacteria, genealogical analyses have been very fruitful in uncovering sex where sexual stages had not been seen, and cryptic species where only one taxon had been recorded (1-4). Quantifying the different aspects of the life cycle, however, has been difficult. Population genomic data now allow accurate measures of mutational and recombinational diversity, and theory predicts that these parameters can be used to estimate the frequencies of different modes of reproduction in the life cycle, including frequencies of sex, outcrossing, and various forms of inbreeding.The bakers' yeast Saccharomyces cerevisiae has long been a model system in genetics and cell biology; more recently, together with its undomesticated relatives Saccharomyces paradoxus and Saccharomyces cariocanus, it is also becoming a focus of studies in ecology and evolution (5-7). Laboratory studies indicate that when conditions are good the primary mode of reproduction is vegetative budding of diploid cells. Starvation induces meiosis, each diploid cell producing a tetrad of haploid spores of two different mating types (a and ␣), enclosed within an ascus (8). When conditions improve, the spores germinate and are constitutively ready to...

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“…DNA (8 g) was labeled and hybridized to 1.0R yeast tiling arrays (Affymetrix, Santa Clara, CA) as described previously (Gresham et al, 2006), except that fragmentation was accomplished by digestion with 0.05 U of DNaseI (Invitrogen, Carlsbad, CA) for 2 min at 37°C. Raw microarray data for individual time points was analyzed with Affymetrix Tiling Analysis Software, version 1.1 with settings as described previously (Lee et al, 2007).…”

Section: Microarray Hybridization and Data Analysismentioning

confidence: 99%

Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae

Zawadzki

Morozov

Broach

2009

MBoC

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Several well-studied promoters in yeast lose nucleosomes upon transcriptional activation and gain them upon repression, an observation that has prompted the model that transcriptional activation and repression requires nucleosome remodeling of regulated promoters. We have examined global nucleosome positioning before and after glucose-induced transcriptional reprogramming, a condition under which more than half of all yeast genes significantly change expression. The majority of induced and repressed genes exhibit no change in promoter nucleosome arrangement, although promoters that do undergo nucleosome remodeling tend to contain a TATA box. Rather, we found multiple examples where the pre-existing accessibility of putative transcription factor binding sites before glucose addition determined whether the corresponding gene would change expression in response to glucose addition. These results suggest that selection of appropriate transcription factor binding sites may be dictated to a large extent by nucleosome prepositioning but that regulation of expression through these sites is dictated not by nucleosome repositioning but by changes in transcription factor activity. INTRODUCTIONChromatin, whose basic unit is a nucleosome that consists of 147 base pairs of DNA wrapped twice around a histone octamer, plays a central role in the regulation of genes. Several experiments in yeast have shown that nucleosome depletion causes derepression of PHO5, GAL1, CUP1, SUC2, and HIS3 in the absence of their transcriptional activators Durrin et al., 1992;Hirschhorn et al., 1992). These observations suggested that nucleosomes in promoters can function as nonspecific repressors, consistent with the concept that DNA sequences incorporated into nucleosomes are less accessible to DNA binding proteins such as transcription factors (Morse, 2003(Morse, , 2007. Subsequent observations have demonstrated that chromatin structure can participate actively in gene regulation through repositioning of nucleosomes so as to block access of a transcription factor to its cognate binding sites or to remove a barrier to such access. Consistent with this notion, several examples have been reported in which gene induction involves recruitment to a promoter of chromatin remodeling factors and histone modifying activities designed to remove or reposition a nucleosome to allow access to an otherwise masked transcription factor binding site (Li et al., 2007;Williams and Tyler, 2007). For example, remodeling factors act at the above-mentioned promoters for PHO5, GAL1, CUP1, and SUC2 to facilitate nucleosome loss on transcriptional activation and conversely to assemble or stabilize nucleosomes on the gene promoter during transcriptional repression (Almer et al., 1986;Fedor and Kornberg, 1989;Shen et al., 2001;Kim et al., 2006).Chromatin can also play a more passive role in gene regulation by simply controlling which transcription factor binding sites are available for participation in gene regulation. Recent genome-wide studies of nucleosome positioning fo...

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Genome-Wide Detection of Polymorphisms at Nucleotide Resolution with a Single DNA Microarray

Cited by 236 publications

References 29 publications

Influence of genotype and nutrition on survival and metabolism of starving yeast

Influence of genotype and nutrition on survival and metabolism of starving yeast

Population genomics of the wild yeast Saccharomyces paradoxus : Quantifying the life cycle

Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae

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