Emerging technologies in yeast genomics (original) (raw)
Fleischmann, R. D. et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science269, 496– 512 (1995). ArticleCAS Google Scholar
Hieter, P. & Boguski, M. Functional genomics: it's all how you read it. Science278, 601– 602 (1997). ArticleCAS Google Scholar
Costanzo, M. C. et al. The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res.28, 73–76 ( 2000). ArticleCAS Google Scholar
Bassett, D. E., Boguski, M. S. & Hieter, P. Yeast genes and human disease. Nature379, 589–590 (1996). ArticleCAS Google Scholar
Bassett, D. E. et al. Genome cross-referencing and XREFdb: implications for the identification and analysis of genes mutated in human disease. Nature Genet.15, 339–344 (1997). ArticleCAS Google Scholar
Venter, J. C. et al. The sequence of the human genome. Science291, 1304–1351 (2001). ArticleCAS Google Scholar
The Genome International Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature409, 860–921 (2001).
Oliver, S. G. From DNA sequence to biological function. Nature379 , 597–600 (1996). ArticleCAS Google Scholar
Devine, S. E. & Boeke, J. D. Efficient integration of artificial transposons into plasmid targets in vitro: a useful tool for DNA mapping, sequencing and genetic analysis. Nucleic Acids Res.22, 3765–3772 (1994). ArticleCAS Google Scholar
Garfinkel, D. J. Insertional mutagenesis by Ty elements in Saccharomyces cerevisiae. Methods Mol. Biol.53, 227–237 (1996). CASPubMed Google Scholar
Gwinn, M. L., Stellwagen, A. E., Craig, N. L., Tomb, J.-F. & Smith, H. O. In vitro TN7 mutagenesis of Haemophilus influenzae Rd and characterization of the role of atpA in transformation. J. Bacteriol.179, 7315– 7320 (1997). ArticleCAS Google Scholar
Burns, N. et al. Large-scale characterization of gene expression, protein localization and gene disruption in Saccharomyces cerevisiae. Genes Dev.8, 1087–1105 ( 1994). ArticleCAS Google Scholar
Smith, V., Botstein, D. & Brown, P. O. Genetic footprinting: a genomic strategy for determining a gene's function given its sequence. Proc. Natl Acad. Sci. USA92, 6479–6483 ( 1995). ArticleCAS Google Scholar
Ross-Macdonald, P., Sheehan, A., Roeder, G. S. & Snyder, M. A multipurpose transposon system for analyzing protein production, localization, and function in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA94, 190–195 ( 1997). ArticleCAS Google Scholar
Ross-MacDonald, P. et al. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature402, 413– 418 (1999).The use of shuttle mutagenesis with multipurpose transposons in a genome-wide analysis of disruption phenotypes, gene expression and protein localization. ArticleCAS Google Scholar
Hoekstra, M. F. et al. A Tn3 derivative that can be used to make short in-frame insertions within genes. Proc. Natl Acad. Sci. USA88, 5457–5461 (1991). ArticleCAS Google Scholar
Biery, M. C., Stewart, F. J., Stellwagen, A. E., Raleigh, E. A. & Craig, N. L. A simple in vitro Tn7-based transposition system with low target site selectivity for genome and gene analysis. Nucleic Acids Res.28, 1067–1077 (2000). ArticleCAS Google Scholar
Seifert, H. S., Chen, E. Y., So, M. & Heffron, F. Shuttle mutagenesis: a method of transposon mutagenesis for Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA83, 735– 739 (1986). ArticleCAS Google Scholar
Ross-Macdonald, P., Sheehan, A., Friddle, C., Roeder, G. S. & Snyder, M. Transposon mutagenesis for the analysis of protein production, function, and localization. Methods Enzymol.303, 512–532 (1999). ArticleCAS Google Scholar
Kumar, A., des Etages, S. A., Coelho, P. S. R., Roeder, G. S. & Snyder, M. High-throughput methods for the large-scale analysis of gene function by transposon tagging . Methods Enzymol.328, 550– 574 (2000). ArticleCAS Google Scholar
Chu, S. et al. The transcriptional program of sporulation in budding yeast. Science282, 699–705 ( 1998). ArticleCAS Google Scholar
Kumar, A. et al. TRIPLES: a database of gene function in Saccharomyces cerevisiae . Nucleic Acids Res.28, 81– 84 (2000). ArticleCAS Google Scholar
Davies, C. J. & Hutchison, C. A. Insertion site specificity of the transposon Tn3. Nucleic Acids Res.23, 507–514 (1995). ArticleCAS Google Scholar
Winzeler, E. A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science285 , 901–906 (1999). A report on the progress of an international consortium that disrupted each annotated open reading frame in the yeast genome using a targeted PCR-based gene-deletion strategy. ArticleCAS Google Scholar
Baudin, A., Ozier-Kalogeropoulos, O., Denouel, A., Lacroute, F. & Cullin, C. A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res.21, 3329–3330 (1993). ArticleCAS Google Scholar
Shoemaker, D. D., Lashkari, D. A., Morris, D., Mittmann, M. & Davis, R. W. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy . Nature Genet.14, 450– 456 (1996). ArticleCAS Google Scholar
Hughes, T. R. et al. Widespread aneuploidy revealed by DNA microarray expression profiling. Nature Genet.25, 333– 337 (2000). ArticleCAS Google Scholar
Chan, T.-F., Carvalho, J., Riles, L. & Zheng, X. F. S. A chemical genomics approach toward understanding the global functions of the target of rapamycin protein (TOR). Proc. Natl Acad. Sci. USA97, 13227–13232 (2000). ArticleCAS Google Scholar
Giaever, G. et al. Genomic profiling of drug sensitivities via induced haploinsufficiency . Nature Genet.21, 278– 283 (1999). ArticleCAS Google Scholar
Schena, M., Shalon, D., Davis, R. W. & Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray . Science270, 467–470 (1995). ArticleCAS Google Scholar
Chee, M. et al. Accessing genetic information with high-density DNA arrays. Science274, 610–614 ( 1996). ArticleCAS Google Scholar
DeRisi, J. L., Iyer, V. R. & Brown, P. O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science278, 680–686 (1997). ArticleCAS Google Scholar
Cho, R. J. et al. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell2, 65– 73 (1998). ArticleCAS Google Scholar
Spellman, P. T. et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell9, 3273–3297 (1998). ArticleCAS Google Scholar
Jelinsky, S. A. & Samson, L. D. Global response of Saccharomyces cerevisiae to an alkylating agent. Proc. Natl Acad. Sci. USA96, 1486–1491 (1999). ArticleCAS Google Scholar
Madhani, H. D., Galitski, T., Lander, E. S. & Fink, G. R. Effectors of a developmental mitogen-activated protein kinase cascade revealed by expression signatures of signaling mutants. Proc. Natl Acad. Sci. USA96, 12530–12535 (1999). ArticleCAS Google Scholar
Holstege, F. C. P. et al. Dissecting the regulatory circuitry of a eukaryotic genome . Cell95, 717–728 (1998). ArticleCAS Google Scholar
Hughes, T. R. et al. Functional discovery via a compendium of expression profiles . Cell102, 109–126 (2000). ArticleCAS Google Scholar
Roberts, C. J. et al. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science287, 873–878 (2000). ArticleCAS Google Scholar
Jelinsky, S. A., Estep, P., Church, G. M. & Samson, L. D. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol. Cell. Biol.20, 8157–8167 (2000). ArticleCAS Google Scholar
Iyer, V. R. et al. Genomic binding distribution of the yeast cell-cycle transcription factors SBF and MBF. Nature409, 533– 538 (2001). ArticleCAS Google Scholar
Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science290, 2306–2309 ( 2000).References42and43describe a new genomic approach that combines chromatin immunoprecipitation and microarray hybridization to map the binding sites of chromosomal proteins in vivo. ArticleCAS Google Scholar
Gerton, J. L. et al. Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA97, 11383–11390 (2000). ArticleCAS Google Scholar
Baudat, F. & Nicolas, A. Clustering of meiotic double-strand breaks on yeast chromosome III. Proc. Natl Acad. Sci. USA94, 5213–5218 (1997). ArticleCAS Google Scholar
Fromont-Racine, M., Rain, J. C. & Legrain, P. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nature Genet.16, 277–282 (1997). ArticleCAS Google Scholar
Ito, T. et al. Toward a protein–protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl Acad. Sci. USA97, 1143–1147 ( 2000). ArticleCAS Google Scholar
Uetz, P. et al. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature403, 623–627 (2000).References47and48describe large-scale applications of the two-hybrid approach towards identifying protein–protein interactions in yeast. ArticleCAS Google Scholar
Fields, S. & Song, O. A novel genetic system to detect protein–protein interactions. Nature340, 245– 246 (1989). ArticleCAS Google Scholar
Brent, R. & Finley, R. L. Understanding gene and allele function with two-hybrid methods. Annu. Rev. Genet.31, 663–704 (1997). ArticleCAS Google Scholar
Heyman, J. A. et al. Genome-scale cloning and expression of individual open reading frames using topoisomerase I-mediated ligation. Genome Res.9, 383–392 (1999). CASPubMedPubMed Central Google Scholar
Martzen, M. R. et al. A biochemical genomics approach for identifying genes by the activity of their products. Science286, 1153–1155 (1999). A genome-wide biochemical approach to identifying gene function. ArticleCAS Google Scholar
Arenkov, P. et al. Protein microchips: use for immunoassay and enzymatic reactions . Anal. Biochem.278, 123– 131 (2000). ArticleCAS Google Scholar
MacBeath, G. & Schreiber, S. L. Printing proteins as microarrays for high-throughput function determination. Science289, 1760–1763 (2000). CASPubMed Google Scholar
Zhu, H. et al. Analysis of yeast protein kinases using protein chips. Nature Genet.26, 283–289 (2000).References53–55describe three new protein microarray methodologies for high-throughput protein analysis. ArticleCAS Google Scholar
Futcher, B., Latter, G. I., Monardo, P., McLaughlin, C. S. & Garrels, J. I. A sampling of the yeast proteome . Mol. Cell. Biol.19, 7357– 7368 (1999). ArticleCAS Google Scholar
Perrot, M. et al. Two-dimensional gel protein database of Saccharomyces cerevisiae (update 1999). Electrophoresis20, 2280–2298 (1999). ArticleCAS Google Scholar
Wigge, P. A. et al. Analysis of the Saccharomyces spindle pole by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. J. Cell Biol.141, 967–977 ( 1998). ArticleCAS Google Scholar
Rout, M. P. et al. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol.148, 635–651 (2000). ArticleCAS Google Scholar
Link, A. J. et al. Direct analysis of protein complexes using mass spectrometry . Nat Biotechnol.17, 676– 682 (1999). ArticleCAS Google Scholar
Gygi, S. P. et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol.17, 994– 999 (1999). A powerful approach to quantitative protein analysis using isotope-coded affinity tags and mass spectrometry. ArticleCAS Google Scholar
Raamsdonk, L. M. et al. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat Biotechnol.19, 45–50 (2001). ArticleCAS Google Scholar
Pease, A. C. et al. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl Acad. Sci. USA91, 5022–5026 (1994). ArticleCAS Google Scholar
Marton, M. J. et al. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nature Med.4 , 1293–1301 (1998). ArticleCAS Google Scholar
Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA95, 14863– 14868 (1998). ArticleCAS Google Scholar
Tamayo, P. et al. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl Acad. Sci. USA96, 2907– 2912 (1999). ArticleCAS Google Scholar
Everitt, B. Cluster Analysis Vol. 122 (Heinemann, London, 1974). Google Scholar
Heyer, L. J., Kruglyak, S. & Yooseph, S. Exploring expression data: identification and analysis of coexpressed genes. Genome Res.9, 1106 –1115 (1999). ArticleCAS Google Scholar
Brown, M. P. et al. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl Acad. Sci. USA97, 262–267 (2000). ArticleCAS Google Scholar
Tavazoie, S., Hughes, J. D., Campbell, M. J., Cho, R. J. & Church, G. M. Systematic determination of genetic network architecture. Nature Genet.22, 281–285 (1999). ArticleCAS Google Scholar