Systematic discovery of new genes in the Saccharomyces cerevisiae genome

Genome Research

Volumn 13, Issue 2, 2003, Pages 264-271

  Kessler, Marco M ^a   Zeng, Qiandong ^a   Hogan, Sarah ^a   Cook, Robin ^a   Morales, Arturo J ^a   Cottarel, Guillaume ^a  

^a GENOME THERAPEUTICS CORPORATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; CAENORHABDITIS ELEGANS PROTEIN; DROSOPHILA PROTEIN; PROTEIN;

ARTICLE; COMPARATIVE GENE MAPPING; COMPUTER MODEL; CONTROLLED STUDY; FUNGAL GENETICS; GENE DISRUPTION; GENE IDENTIFICATION; GENETIC CODE; GENETIC TRANSCRIPTION; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEOMICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; VALIDATION PROCESS; AMINO ACID SEQUENCE; ANIMAL; CATTLE; CHROMOSOME; CHROMOSOME MAP; COMPARATIVE STUDY; FUNGAL GENE; GENETICS; GENOME; HUMAN; METHODOLOGY; MOLECULAR GENETICS; MOUSE; NUCLEOTIDE SEQUENCE; VALIDATION STUDY;

FUNGI; MYXOGASTRIA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

AMINO ACID SEQUENCE; ANIMALS; CAENORHABDITIS ELEGANS PROTEINS; CATTLE; CHROMOSOME MAPPING; CHROMOSOMES, FUNGAL; CONSERVED SEQUENCE; DROSOPHILA PROTEINS; GENES, FUNGAL; GENOME, FUNGAL; HUMANS; MICE; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PROTEINS; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0037315819     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.232903     Document Type: Article

References (26)

1. Andrade, M.A., Daruvar, A., Casari, G., Schneider, R., Termier, M., and Sander, C. 1997. Characterization of new proteins found by analysis of short open reading frames from the full yeast genome. Yeast 13: 1363-1374.
2. 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.
3. 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.
4. Brown, C.E., Tarun Jr., S.Z., Boeck, R., and Sachs, A. 1996. PAN3 encodes a subunit of the Pab1p-dependent poly(A) nuclease in Saccharomyces cerevisiae. Mol. Cell. Biol 16: 5744-5753.
5. 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.
6. Erdeniz, N., Mortensen, U.H., and Rothstein, R. 1997. Cloning-free PCR-based allele replacement methods. Genome Res. 7: 1174-1183.
7. 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: 546-567.
8. Gopal, S., Schroeder, M., Pieper, U., Sczyrba, A., Aytekin-Kurban, G., Bekiranov, S., Fajardo, J.E., Eswar, N., Sanchez, R., Sali, A., et al. 2001. Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome. Nat. Genet. 27: 337-340.
9. Graber, J.H., McAllister, G.D., and Smith, T.F. 2002. Probabilistic prediction of Saccharomyces cerevisiae mRNA 3′-processing sites. Nucleic Acids Res. 30: 1851-1858.
10. Guthrie, C., Fink, G.R., Simon, M.I., and Abelson, J.N., Eds. 1991. Guide to yeast genetics and molecular biology. Methods Enzymol. Vol. 194. Academic Press, New York, NY.
11. Hector, R.E., Nykamp, K.R., Dheur, S., Anderson, J.T., Non, P.J., Urbinati, C.R., Wilson, S.M., Minvielle-Sebastia, L., and Swanson, M.S. 2002. Dual requirement for yeast hnRNP Nab2p in mRNA poly(A) tail length control and nuclear export. EMBO J. 21: 1800-1810.
12. Hughes, J.D., Extep, P.W., Tavazoie, S., and Church, G.M. 2000. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296: 1205-1214.
13. Johnston, M., Hillier, L., Riles, L., Albermann, K., Andre, B., Ansorge, W., Benes, V., Bruckner, M., Delius, H., Dubois, E., et al. 1997. The nucleotide sequence of Saccharomyces cerevisiae chromosome XII. Nature 387: 87-90.
14. 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.
15. Kupfer, D.M., Reece, C.A., Clifton, S.W., Roe, B.A., and Prade, R.A. 1997. Multicellular ascomycetous fungal genomes contain more than 8000 genes. Fungal Genet. Biol. 21: 364-372.
16. Mackiewicz, P., Kowalczuk, M., Mackiewicz, D., Nowicka, A., Dudkiewicz, M., Laszkiewicz, A., Dudek, M.R., and Cebrat, S. 2002. How many protein-coding genes are there in the Saccharomyces cerevisiae genome? Yeast 19: 619-629.
17. Mewes, H.W., Albermann, K., Bahr, M., Frishman, D., Gleissner, A., Hani, J., Heumann, K., Kleine, K., Maierl, A., Oliver, S.G., et al. 1997. Overview of the yeast genome. Nature 387: 7-65.
18. Nicholas, K.B., Nicholas Jr., H.B., and Deerfield II, D.W. 1997. GeneDoc: Analysis and visualization of genetic variation. EMBnet News 4:14-17. http://www.no.embnet.org/embnet.news/vol4contents.html
19. Olivas, W.M., Muhlrad, D., and Parker, R. 1997. Analysis of the yeast genome: Identification of new noncoding and small ORF-containing RNAs. Nucleic Acids Res. 25: 4619-4625.
20. Reboul, J., Vaglio, P., Tzellas, N., Thierry-Mieg, N., Moore, T., Jackson, C., Shin-I, T., Kohara, Y., Thierry-Mieg, D., Thierry-Mieg, J., et al. 2001. Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans. Nat. Genet. 27: 332-336.
21. 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.
22. Thomas, B.J. and Rothstein, R. 1989. The genetic control of direct-repeat recombination in Saccharomyces: The effect of rad52 and rad1 on mitotic recombination at GAL 10, a transcriptionally regulated gene. Genetics 123: 725-738.
23. Tzung, K.W., Williams, R.M., Scherer, S., Federspiel, N., Jones, T., Hansen, N., Bivolarevic, V., Huizar, L., Komp, C., Surzycki,. R., et al. 2001. Genomic evidence for a complete sexual cycle in Candida albicans. Proc. Natl. Acad. Sci. 98: 3249-3253.
24. 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.
25. Winzeler, E.A. and Davis, R.W. 1997. Functional analysis of the yeast genome. Curr. Opin. Genet. Dev. 7: 771-776.
26. Zeng, Q., Morales, A., and Cottarel, G. 2001. Fungi and humans: Closer than you think. Trends Genet. 17: 682-684.