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  • Review Article
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Emerging technologies in yeast genomics

Nature Reviews Genetics volume 2, pages 302–312 (2001)Cite this article

Key Points

  • Genomic technologies have altered the way in which we use molecular biology; the budding yeast Saccharomyces cerevisiae, because of its compact genome and tractable genetics, has emerged as a preferred model for developing these new technologies.

  • This review discusses the most promising of these emerging technologies, which include:

  • The use of multipurpose transposons to generate genome-wide insertional mutations to study gene expression, gene function and protein localization.

  • The development of microarray technology to study genome-wide changes in the expression of all annotated yeast genes during certain biological processes or conditions, and for systematically mapping the chromosomal binding sites of DNA-binding proteins.

  • The use of large-scale two-hybrid studies to generate a global protein–protein interaction map in yeast.

  • The application of biochemical genomics to generating proteins and to assaying their functions on a genome-wide scale.

  • New approaches to generating protein microarrays, which allow functionally active proteins to be fixed onto a solid support for large-scale functional analysis.

  • The use of mass spectrometry to identify proteins in complex protein mixtures.

  • These approaches have benefited from bioinformatic resources that are widely available to the yeast genetics community, such as curated databases and online data sets, which, in the future, will help to continue the rapid rate at which new yeast genomics technologies are developed.

Abstract

The genomic revolution is undeniable: in the past year alone, the term 'genomics' was found in nearly 500 research articles, and at least 6 journals are devoted solely to genomic biology. More than just a buzzword, molecular biology has genuinely embraced genomics (the systematic, large-scale study of genomes and their functions). With its facile genetics, the budding yeast Saccharomyces cerevisiae has emerged as an important model organism in the development of many current genomic methodologies. These techniques have greatly influenced the manner in which biology is studied in yeast and in other organisms. In this review, we summarize the most promising technologies in yeast genomics.

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Figure 1: Multipurpose transposons.
Figure 2: PCR-based gene-deletion strategy.
Figure 3: Genome-wide identification of protein–DNA interactions.
Figure 4: Two-hybrid assays.
Figure 5: Protein microrrays.

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Acknowledgements

A.K. is supported by a postdoctoral fellowship from the American Cancer Society.

Author information

Authors and Affiliations

  1. Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven , 06520-8103, Connecticut, USA

    Anuj Kumar & Michael Snyder

Authors
  1. Anuj Kumar
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Supplementary information

Related links

Related links

DATABASE LINKS

Tor1

Tor2

MAPK

TFIID

Srb5

Srb10

erg2

Rpn4

Swi4

Swi6

Mbp1

Gal4

Ste12

Spo11

GAL1

GST

GAL10

ADH2

Saccharomyces Genome Database (SGD) (Function Junction)

Yeast Proteome Database (YPD)

Munich Information Centre for Protein Sequences (MIPS)

Transposon mutagenesis/tagging

Yeast Genome Deletion Project

Stanford cell-cycle microarray data set

Stanford Mircroarray Database

Rick Young's microarray data set

Curagen's Gene Scape Portal

Stan Field's two-hybrid data set

Yeast protein function assignment

FURTHER INFORMATION

NCBI's Entrez Genome site

Affymetrix, Inc.

Rosetta Inpharmatics

ENCYCLOPEDIA OF LIFE SCIENCES

Saccharomyces cerevisiae: Applications

Mass spectroscopy in biology

Multispot array technologies

Glossary

FUNCTIONAL GENOMICS

The development and systematic application of experimental methodologies to analyse gene function on a genome-wide scale.

TRANSPOSON

Mobile DNA elements that can relocate within the genome of their hosts; transposons can be used for various applications, including insertional mutagenesis, gene identification, gene tagging and DNA sequencing.

EPITOPE

Part of a protein (antigen) that combines with the antigen-binding site of an antibody; the incorporation of an epitope-encoding sequence into a target gene is called epitope-tagging.

SHUTTLE MUTAGENESIS

A method in which cloned yeast genes are mutated by bacterial transposition in Escherichia coli; mutant alleles are subsequently introduced ('shuttled') into yeast where they integrate at their corresponding genomic loci by homologous recombination.

CONDITIONAL MUTATIONS

Mutations that generate an observable mutant phenotype under a given set of growth conditions (restrictive conditions), but no mutant phenotype (or a reduced phenotype) under a separate set of conditions (permissive conditions).

ESSENTIAL GENE

A gene that is indispensable for cell viability under defined growth conditions; complete loss of the function of an essential gene is lethal.

HETEROZYGOUS DIPLOID

A diploid yeast cell with different alleles at a particular locus. Heterozygous diploid cells can be used to ascribe cellular functions to essential genes.

HAPLOINSUFFICIENCY

When loss of function of one gene copy leads to a mutant phenotype.

PROTEOMICS

The development and systematic application of experimental methodologies to analyse the entire protein complement of an organism (its 'proteome').

CONTACT PRINTING

A method of microarray generation in which samples are spotted onto a slide using specialized spring-loaded printing tips; liquid is drawn up into the printing tip by capillary action and subsequently deposited on contact with the surface of the slide.

PEPTIDE LIBRARIES

A collection of small polypeptides that might be used to assay protein function.

ISOELECTRIC POINT

The pH at which a molecule is electrically neutral (the sum of its positive charges equals the sum of its negative charges).

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Kumar, A., Snyder, M. Emerging technologies in yeast genomics. Nat Rev Genet 2, 302–312 (2001). https://doi.org/10.1038/35066084

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