Parallel identification of new genes in Saccharomyces cerevisiae

Genome Research

Volumn 13, Issue 1, 2003, Pages 1210-1220

  Oshiro, Guy ^a   Wodicka, Lisa M ^b   Washburn, Michael P ^c   Yates III, John R ^c,d   Lockhart, David J ^b,e   Winzeler, Elizabeth A ^a,d  

^a GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^b Aventa Biosciences Corporation   (United States)

^c SYNGENTA BIOTECHNOLOGY INC   (United States)

^d SCRIPPS RESEARCH INSTITUTE   (United States)

^e SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ANIMAL CELL; CONTROLLED STUDY; EXPERIMENTATION; FUNGAL GENETICS; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC TRANSCRIPTION; MASS SPECTROMETRY; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; REVIEW; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE;

ANIMALIA; FUNGI; MYXOGASTRIA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0037224550     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (35)

1. Arnold, I., Pfeiffer, K., Neupert, W., Stuart, R.A., and Schagger, H. 1998. Yeast mitochondrial F1F0-ATP synthase exists as a dimer: Identification of three dimer-specific subunits. Embo J 17: 7170-7178.
2. Basrai, M.A., Hieter, P., and Boeke, J.D. 1997. Small open reading frames: Beautiful needles in the haystack. Genome Res. 7: 768-771.
3. Basrai, M.A., Velculescu, V.E., Kinzler, K.W., and Hieter, P. 1999. NORF5/HUG1 is a component of the MEC1-mediated checkpoint response to DNA damage and replication arrest in Saccharomyces cerevisiae. Mol. Cell Biol. 19: 7041-7049.
4. Blandin, G., Durrens, P., Tekaia, F., Aigle, M., Bolotin-Fukuhara, M., Bon, E., Casaregola, S., de Montigny, J., Gaillardin, C., Lepingle, A. et al. 2000. Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited. FEBS Lett 487: 31-36.
5. Cherry, J.M., Adler, C., Ball, C., Chervitz, S.A., Dwight, S.S., Hester, E.T., Jia, Y., Juvik, G., Roe, T., Schroeder, M. et al. 1998. SGD: Saccharomyces Genome Database. Nucleic Acids Res. 26: 73-79.
6. Cho, R.J., Campbell, M.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E., Landsman, D., Lockhart, D.J. et al. 1998. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2: 65-73.
7. Cliften, P.F., Hillier, L.W., Fulton, L., Graves, T., Miner, T., Gish, W.R., Waterston, R.H., and Johnston, M. 2001. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res. 11: 1175-1186.
8. Cohen, B.A., Mitra, R.D., Hughes, J.D., and Church, G.M. 2000. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat. Genet. 26: 183-186.
9. Elledge, S.J., Zhou, Z., Allen, J.B., and Navas, T.A. 1993. DNA damage and cell cycle regulation of ribonucleotide reductase. Bioessays 15: 333-339.
10. Eng, J.K., McCormack, A.L., and Yates, J.R.I. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5: 976-989.
11. Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J.D., Jacq, C., Johnston, M. et al. 1996. Life with 6000 genes. Science 274: 546, 563-567.
12. Huang, M. and Elledge, S.J. 1997. Identification of RNR4, encoding a second essential small subunit of ribonucleotide reductase in Saccharomyces cerevisiae. Mol. Cell Biol. 17: 6105-6113.
13. Hughes, T.R., Marton, M.J., Jones, A.R., Roberts, C.J., Stoughton, R., Armour, C.D., Bennett, H.A., Coffey, E., Dai, H., He, Y.D. et al. 2000. Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
14. Jelinsky, S.A. and Samson, L.D. 1999. Global response of Saccharomyces cerevisiae to an alkylating agent. Proc. Natl. Acad. Sci. 96: 1486-1491.
15. Jelinsky, S.A., Estep, P., Church, G.M., and Samson, L.D. 2000. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: rpn4 links base excision repair with proteasomes. Mol. Cell Biol. 20: 8157-8167.
16. Kapranov, P., Cawley, S.E., Drenkow, J., Bekiranov, S., Strausberg, R.L., Fodor, S.P., and Gingeras, T.R. 2002. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296: 916-919.
17. Kiser, G.L. and Weinert, T.A. 1996. Distinct roles of yeast MEC and RAD checkpoint genes in transcriptional induction after DNA damage and implications for function. Mol. Biol. Cell 7: 703-718.
18. Kumar, A., Harrison, P.M., Cheung, K.H., Lan, N., Echols, N., Bertone, P., Miller, P., Gerstein, M.B., and Snyder, M. 2002. An integrated approach for finding overlooked genes in yeast. Nat. Biotechnol. 20: 58-63.
19. Kurtz, S. and Shore, D. 1991. RAP1 protein activates and silences transcription of mating-type genes in yeast. Genes Dev. 5: 616-628.
20. Lockhart, D.J. and Winzeler, E.A. 2000. Genomics, gene expression and DNA arrays. Nature 405: 827-836.
21. Mannhaupt, G., Schnall, R., Karpov, V., Vetter, I., and Feldmann, H. 1999. Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast. FEBS Lett 450: 27-34.
22. Mewes, H.W., Albermann, K., Heumann, K., Liebl, S., and Pfeiffer, F. 1997. MIPS: A database for protein sequences, homology data and yeast genome information. Nucleic Acids Res. 25: 28-30.
23. Mewes, H.W., Heumann, K., Kaps, A., Mayer, K., Pfeiffer, F., Stocker, S., and Frishman, D. 1999. MIPS: A database for genomes and protein sequences. Nucleic Acids Res. 27: 44-48.
24. Moehle, C.M. and Hinnebusch, A.G. 1991. Association of RAP1 binding sites with stringent control of ribosomal protein gene transcription in Saccharomyces cerevisiae. Mol. Cell Biol. 11: 2723-2735.
25. Olivas, W.M., Muhlrad, D., and Parker, R. 1997. Analysis of the yeast genome: Identification of new non-coding and small ORF-containing RNAs. Nucleic Acids Res. 25: 4619-4625.
26. Ozsarac, N., Straffon, M.J., Dalton, H.E., and Dawes, I.W. 1997. Regulation of gene expression during meiosis in Saccharomyces cerevisiae: SPR3 is controlled by both ABFI and a new sporulation control element. Mol. Cell Biol. 17: 1152-1159.
27. Pease, A.C., Solas, D., Sullivan, E.J., Cronin, M.T., Holmes, C.P., and Fodor, S.P. 1994. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. 91: 5022-5026.
28. Rittberg, D.A. and Wright, J.A. 1989. Relationships between sensitivity to hydroxyurea and 4-methyl-5-amino-1-formylisoquinoline thiosemicarbazone (MAIO) and ribonucleotide reductase RNR2 mRNA levels in strains of Saccharomyces cerevisiae. Biochem. Cell Biol. 67: 352-357.
29. Ross-Macdonald, P., Coelho, P.S., Roemer, T., Agarwal, S., Kumar, A., Jansen, R., Cheung, K.H., Sheehan, A., Symoniatis, D., Umansky, L. et al. 1999. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402: 413-418.
30. Sharp, P.M. and Li, W.H. 1987. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15: 1281-1295.
31. Shoemaker, D.D., Schadt, E.E., Armour, C.D., He, Y.D., Garrett-Engele, P., McDonagh, P.D., Loerch, P.M., Leonardson, A., Lum, P.Y., Cavet, G. et al. 2001. Experimental annotation of the human genome using microarray technology. Nature 409: 922-927.
32. Velculescu, V.E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M.A., Bassett, Jr., D.E., Hieter, P., Vogelstein, B., and Kinzler, K.W. 1997. Characterization of the yeast transcriptome. Cell 88: 243-251.
33. Washburn, M.P., Wolters, D., and Yates, 3rd, J.R., 2001. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19: 242-247.
34. Wodicka, L., Dong, H., Mittmann, M., Ho, M.H., and Lockhart, D.J. 1997. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotechnol. 15: 1359-1367.
35. Wolters, D.A., Washburn, M.P., and Yates, 3rd, J.R. 2001. An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73: 5683-5690.