Abstract
The Schizosaccharomyces pornbe genome sequence and a preliminary analysis have been reported (Wood et al. 2002). This landmark will further establish and expand the role of fission yeast as a major experimental model organism. The sequencing phase is almost complete, with only four gaps remaining in the repetitive centromeric and telomeric regions. As noted for similar regions in other organisms, these are proving difficult to complete. Work is continuing to finish the sequence to the telomeric repeats, thus precluding genes being missed. The published genome sequence also excludes the rDNA repeats, known to be present as two tandem arrays on chromosome III (Schaak et al. 1982). Below and in Table 2.1, some of the most notable features of the fission yeast genome sequence are summarized.
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References
Altman RB, Raychaudhuri S (2001) Whole-genome expression analysis: challenges beyond clustering. Curr Opin Structural Biol 11: 340–347
Aravind L, Watanabe H, Lipman DJ, Koonin EV (2000) Lineage-specific loss and divergence of functionally linked genes in eukaryotes. Proc Natl Acad Sci USA 97: 11319–11324
Ball CA, Jin H, Sherlock G et al. (2001) Saccharomyces genome database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res 29: 80–81
Bolton SJ, Gartner A, Reboul J et al. (2002) Combined functional genomic maps of the C. elegans DNA damage response. Science 295: 127–131
Brazma A, Hingamp P, Quackenbush J et al. (2001) Minimum information about a microarray experiment ( MIAME) - toward standards for microarray data. Nat Genet 29: 365–371
Brent R (2000) Genomic Biology. Cell 100: 169–183
Brown PO, Botstein D (1999) Exploring the new world of the genome with DNA microarrays. Nat Genet 21: 33–37
Carroll SB, Grenier JK, Weatherbee SD (2001) From DNA to diversity. Blackwell, Malden, Massachusetts
Chen D, Toone WM, Mata J et al. (2003) Global transcriptional responses of fission yeast to environmental stress. Mol Biol Cell 14: 214–229
Claverie JM (2001) What if there are only 30,000 human genes? Science 291: 1255–1257
Colman-Lerner A, Chin TE, Brent R (2001) Yeast Cbkl and Mob2 activate daughter-specific genetic programs to induce asymmetric cell fates. Cell 107: 739–750
Costanzo MC, Crawford ME, Hirschman JE et al. (2001) YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res 29: 75–79
Crom SL, Devaux F, Jacq C, Marc P (2002) yMGV: helping biologists with yeast microarray data mining. Nucleic Acids Res 30: 76–79
Decottignies A, Sanchez-Perez I, Nurse P (2003) Schizosaccharomyces pombe essential genes: a pilot study. Genome Res 13: 399–406
Delneri D, Brancia FL, Oliver SG (2001) Towards a truly integrative biology through the functional genomics of yeast. Curr Opin Biotechnol 12: 87–91
Ding DQ, Tornita Y, Yamamoto A et al. (2000) Large-scale screening of intracellular protein localization in living fission yeast cells by the use of a GFP-fusion genomic DNA library. Genes Cells 5: 169–190
Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14863–14868
Enard W, Khaitovich P, Klose J et al. (2002) Intra-and interspecific variation in primate gene expression patterns. Science 296: 340–343
Fan J, Yang X, Wang W et al. (2002) Global analysis of stress-regulated mRNA turnover by using cDNA arrays. Proc Natl Acad Sci USA 99: 10611–10616
Ferea TL, Brown PO (1999) Observing the living genome. Curr Opin Genet Dev 9: 715–722
Fraser AG, Kamath RS, Zipperlen P et al. (2000) Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408: 325–330
Ge H, Liu Z, Church GM, Vidal M (2001) Correlation between transcriptome and interactome mapping data from S. cerevisiae. Nat Genet 29: 482–486
Goffeau A (2000) Four years of post-genomic life with 6,000 yeast genes. FEBS Lett 480: 3741
Hartwell L, Hopfield J, Leibler S, Murray A (1999) From molecular to modular cell biology. Nature 402: C47–052
Hughes TR, Marton MJ, Jones AR et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109–126
Ideker T, Thorsson V, Ranish JE et al. (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292: 929–934
Jansen R, Greenbaum D, Gerstein M (2002) Relating whole-genome expression data with protein-protein interactions. Genome Res 12: 37–46
Krupp G, Cherayil B, Frendewey D et al. (1986) Two RNA species co-purify with RNase P from the fission yeast S. pombe. EMBO J 5: 1697–1703
Kumar A, Snyder M (2001) Emerging technologies in yeast genomics. Nat Rev Genet 2: 30 2312
Kumar A, Snyder M (2002) Protein complexes take the bait. Nature 415: 123–124
Lee TI, Rinaldi NJ, Robert F et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799–804
Lockhart D, Winzeler E (2000) Genomics, gene expression and DNA arrays. Nature 405: 827–836
Marc P, Devaux F, Jacq C (2001) yMGV: a database for visualization and data mining of published genome-wide yeast expression data. Nucleic Acids Res 29: e63
Mata J, Lyne R, Burns G, Bähler J (2002) The transcriptional program of meiosis and sporulation in fission yeast. Nature Genet 32: 143–147
Mewes HW, Albermann K, Bahr M et al. (1997) Overview of the yeast genome. Nature 387: 7–65
Nal B, Mohr E, Ferrier P (2001) Location analysis of DNA-bound proteins at the whole-genome level: untangling transcriptional regulatory networks. BioEssays 23: 473–476
Ohler U, Niemann H (2001) Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet 17: 56–60
Pilpel Y, Sudarsanam P, Church GM (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet 29: 153–159
Pradet-Balade B, Boulme F, Beug H et aí. (2001) Translational control: bridging the gap between genomics and proteomics. Trends Biochem Sci 26: 225–229
Ribes V, Dehoux P, Tollervey D (1988) 7SL RNA from S. pombe is encoded by a single copy essential gene. EMBO J 7: 231–237
Roberts CJ, Nelson B, Marton MJ et al. (2000) Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287: 873–880
Rutherford K, Parkhill J, Crook J et al. (2000) Artemis: sequence visualization and annotation. Bioinformatics 16: 944–945
Schaak J, Mao J, Söll D (1982) The 5.8S RNA gene sequence and the ribosomal repeat of S. pombe. Nucleic Acids Res 10: 2851–2864
Stillman B (2001) Genomic views of genome duplication. Science 294: 2301–2304
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
The C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:2012–2018
Tong AH, Evangelista M, Parsons AB et al. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364–2368
Tong AH, Drees B, Nardelli G et al. (2002) A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295: 321–324
Toth A, Rabitsch KP, Galova M et al. (2000) Functional genomics identifies monopolin: a kinetochore protein required for segregation of homologs during meiosis I. Cell 103: 11551168
Tupler R, Perini G, Green MR (2001) Expressing the human genome. Nature 409: 832–833
Vidal M (2001) A biological atlas of functional maps. Cell 104: 333–339
Wang Y, Liu CL, Storey JD et al. (2002) Precision and functional specificity in mRNA decay. Proc Natl Acad Sci USA 99: 5860–5865
Watanabe Y, Yamamoto M (1994) S. pombe mei2 + encodes an RNA-binding protein essential for premeiotic DNA synthesis and meiosis I, which cooperates with a novel RNA species meiRNA. Cell 78: 487–498
Watanabe T, Miyashita K, Saito TT et al. (2001) Comprehensive isolation of meiosis-specific genes identifies novel proteins and unusual non-coding transcripts in S. pombe. Nucleic Acids Res 29: 2327–2337
Watanabe T, Miyashita K, Saito TT, Nabeshima K, Nojima H (2002) Abundant poly (A)- bearing RNAs that lack open reading frames in S. pombe. DNA Res 9: 209–215
Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708–713
Wood V, Bähler J (2002) How to get the best from fission yeast genome data. Comp Funct Genom 3: 282–288
Wood V, Rutherford KM, Ivens A et al. (2001) A re-annotation of the S. cerevisiae genome. Comp Funct Genom 2: 143–154
Wood V, Gwilliam R, Rajandream MA et al. (2002) The genome sequence of S. pombe. Nature 415: 871–880
Young R (2000) Biomedical discovery with DNA arrays. Cell 102: 9–16
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Bähler, J., Wood, V. (2004). The Genome and Beyond. In: Egel, R. (eds) The Molecular Biology of Schizosaccharomyces pombe . Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-10360-9_2
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DOI: https://doi.org/10.1007/978-3-662-10360-9_2
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