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  • Review Article
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Treasures and traps in genome-wide data sets: case examples from yeast

Nature Reviews Genetics volume 3, pages 653–661 (2002)Cite this article

Key Points

  • The budding yeast Saccharomyces cerevisiae, because of its compact genome and tractable genetics, has served as a prime model organism for developing and applying large-scale genomic technologies.

  • During the past few years, several comparable genome-wide functional studies have been published. In many cases, the majority of results can be confirmed by completely independent methods, but it has also become apparent that there are limitations and uncertainties associated with these technologies.

  • These problems and possible solutions are discussed by highlighting yeast work in which gene expression, protein abundance, protein–DNA interactions, DNA replication, protein interactions and genome-wide mutagenesis have been investigated.

  • Each method has its own drawbacks and might not be comprehensive.

  • Differences in the genetic background of strains, in experimental set-ups and in analytical methods contribute to inconsistencies between databases. Technical difficulties and experimental variation are also the cause of false-positive and false-negative results. Because of the work involved, some large-scale studies have not been replicated, and appropriate controls might not be feasible. In some cases, it might be difficult to judge the rate of erroneous results.

  • The integration of genome-wide data sets increases fidelity and generates the most relevant information. Computational approaches towards this aim are discussed.

Abstract

Since the publication of the Saccharomyces cerevisiae genome sequence, much effort has been dedicated to developing high-throughput techniques to generate comprehensive information about the function and dynamics of all genes in this yeast's genome. These techniques have generated data sets that typically contain large amounts of reliable and valuable biological information. Nevertheless, there are also uncertainties that are associated with such large-scale studies, which we discuss in this review. These uncertainties increase with the complexity of the organism under study. On the basis of the results from yeast, we should learn much from human and mouse genomic data sets. However, as with yeast data sets, they might also contain misleading results.

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Figure 1: Strain differences in Saccharomyces cerevisiae.
Figure 2: Detecting the interaction sites of DNA-binding proteins by chromatin immunoprecipitation.
Figure 3: Identifying origins of replication by measuring the timing and progression of DNA replication.
Figure 4: Measuring protein–protein interactions.
Figure 5: Method used to construct S. cerevisiae deletion strains systematically.

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Acknowledgements

E.A.W. is supported by a New Scholars Award from The Ellison Medical Foundation. B.G. is supported by a fellowship from the Swiss National Science Foundation.

Author information

Authors and Affiliations

  1. Department of Cell Biology, ICND 202, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, California, USA

    Björn Grünenfelder & Elizabeth A. Winzeler

Authors
  1. Björn Grünenfelder
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  2. Elizabeth A. Winzeler
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Corresponding author

Correspondence to Elizabeth A. Winzeler.

Related links

Related links

DATABASES

<i>Saccharomyces</i> Genome Database

Cln1

Gal4

NEJ1

RNR1

RNR3

Ste12

FURTHER INFORMATION

Munich Information Centre for Protein Sciences — Comprehensive Yeast Genome Database

Saccharomyces Genome Database

Saccharomyces Genome Deletion Project

Transposon-Insertion Phenotypes, Localization and Expression in Saccharomyces (TRIPLES)

Yeast Proteome Database

Glossary

TRANSCRIPTOME

The entire mRNA complement that is expressed by an organism. The expression of mRNA transcripts is dynamic and changes under different conditions.

TWO-DIMENSIONAL GEL

A gel-electrophoresis method by which proteins are separated by charge in the first dimension and by size in the second.

MASS SPECTROMETRY

A technique that provides accurate information about the molecular mass of complex molecules. It can identify extremely small amounts of proteins by their mass-fragment spectra.

CODON-USAGE BIAS

A measurement that takes into account the frequency of less commonly used alternative codons in a protein-coding sequence.

LIQUID CHROMATOGRAPHY

A method that separates molecules from mixtures by selective adsorption.

PHEROMONE

A molecule that is produced for signalling between individuals of the same species.

AUTONOMOUS REPLICATION SEQUENCE

(ARS). A consensus sequence that is necessary, but not sufficient, to allow the replication and maintenance of an otherwise non-replicating plasmid in yeast.

MESELSON–STAHL EXPERIMENT

The experiment that was originally used to prove semiconservative DNA replication. Cells were first grown in a medium that contains heavy isotopes and then moved to a medium that contains light isotopes. The newly replicated DNA was analysed by density-gradient centrifugation. Because only heavy–light hybrids were observed versus heavy- or light-labelled DNA, it was concluded that DNA replicates semi-conservatively.

BAIT

In a yeast two-hybrid approach, this is the protein that is fused to the Gal4 DNA-binding domain.

PREY

In a yeast two-hybrid approach, this is the protein that is fused to the Gal4 activating domain.

ORTHOLOGUE

A homologous gene that originated through speciation.

STOICHIOMETRIC

The molar ratio of interacting molecules.

TETRAD DISSECTION

Phenotypic analysis of the four haploid daughter cells that come from the meiotic cell division of a single diploid cell in yeast. In Saccharomyces cerevisiae, the four meiotic daughter cells are in a single ascus, or spore. Physically associated with one another in this 'tetrad', they can be dissected away from each other, allowing phenotypic segregation ratios to be scored precisely.

SYNTHETIC INTERACTIONS

These occur when a double mutant has a phenotype that is more severe or milder than the phenotype of either single-mutant parent. For suppressors (synthetic viable), the double mutant is viable when at least one of the single mutants is not. For synthetic-lethal mutants, the double mutant is inviable under conditions in which both parental mutations are viable.

COLLATERAL MUTATION

A random second-site mutation that might have been introduced inadvertently during site-directed mutagenesis.

ANEUPLOIDY

The presence of extra copies, or no copies, of some chromosomes.

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Grünenfelder, B., Winzeler, E. Treasures and traps in genome-wide data sets: case examples from yeast. Nat Rev Genet 3, 653–661 (2002). https://doi.org/10.1038/nrg886

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