Skip to main content

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Altman RB, Raychaudhuri S (2001) Whole-genome expression analysis: challenges beyond clustering. Curr Opin Structural Biol 11: 340–347

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Google Scholar 

  • Bolton SJ, Gartner A, Reboul J et al. (2002) Combined functional genomic maps of the C. elegans DNA damage response. Science 295: 127–131

    Article  Google Scholar 

  • 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

    Google Scholar 

  • Brent R (2000) Genomic Biology. Cell 100: 169–183

    Article  PubMed  CAS  Google Scholar 

  • Brown PO, Botstein D (1999) Exploring the new world of the genome with DNA microarrays. Nat Genet 21: 33–37

    Article  PubMed  CAS  Google Scholar 

  • Carroll SB, Grenier JK, Weatherbee SD (2001) From DNA to diversity. Blackwell, Malden, Massachusetts

    Google Scholar 

  • Chen D, Toone WM, Mata J et al. (2003) Global transcriptional responses of fission yeast to environmental stress. Mol Biol Cell 14: 214–229

    Article  PubMed  CAS  Google Scholar 

  • Claverie JM (2001) What if there are only 30,000 human genes? Science 291: 1255–1257

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Crom SL, Devaux F, Jacq C, Marc P (2002) yMGV: helping biologists with yeast microarray data mining. Nucleic Acids Res 30: 76–79

    Google Scholar 

  • Decottignies A, Sanchez-Perez I, Nurse P (2003) Schizosaccharomyces pombe essential genes: a pilot study. Genome Res 13: 399–406

    Google Scholar 

  • Delneri D, Brancia FL, Oliver SG (2001) Towards a truly integrative biology through the functional genomics of yeast. Curr Opin Biotechnol 12: 87–91

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Enard W, Khaitovich P, Klose J et al. (2002) Intra-and interspecific variation in primate gene expression patterns. Science 296: 340–343

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Ferea TL, Brown PO (1999) Observing the living genome. Curr Opin Genet Dev 9: 715–722

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Ge H, Liu Z, Church GM, Vidal M (2001) Correlation between transcriptome and interactome mapping data from S. cerevisiae. Nat Genet 29: 482–486

    Article  PubMed  CAS  Google Scholar 

  • Goffeau A (2000) Four years of post-genomic life with 6,000 yeast genes. FEBS Lett 480: 3741

    Article  Google Scholar 

  • Hartwell L, Hopfield J, Leibler S, Murray A (1999) From molecular to modular cell biology. Nature 402: C47–052

    Article  PubMed  CAS  Google Scholar 

  • Hughes TR, Marton MJ, Jones AR et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109–126

    Article  PubMed  CAS  Google Scholar 

  • Ideker T, Thorsson V, Ranish JE et al. (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292: 929–934

    Article  PubMed  CAS  Google Scholar 

  • Jansen R, Greenbaum D, Gerstein M (2002) Relating whole-genome expression data with protein-protein interactions. Genome Res 12: 37–46

    Article  PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Kumar A, Snyder M (2001) Emerging technologies in yeast genomics. Nat Rev Genet 2: 30 2312

    Google Scholar 

  • Kumar A, Snyder M (2002) Protein complexes take the bait. Nature 415: 123–124

    Article  PubMed  CAS  Google Scholar 

  • Lee TI, Rinaldi NJ, Robert F et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799–804

    Article  PubMed  CAS  Google Scholar 

  • Lockhart D, Winzeler E (2000) Genomics, gene expression and DNA arrays. Nature 405: 827–836

    Article  PubMed  CAS  Google Scholar 

  • 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

    Google Scholar 

  • Mata J, Lyne R, Burns G, Bähler J (2002) The transcriptional program of meiosis and sporulation in fission yeast. Nature Genet 32: 143–147

    Article  PubMed  CAS  Google Scholar 

  • Mewes HW, Albermann K, Bahr M et al. (1997) Overview of the yeast genome. Nature 387: 7–65

    Article  PubMed  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Ohler U, Niemann H (2001) Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet 17: 56–60

    Article  PubMed  CAS  Google Scholar 

  • Pilpel Y, Sudarsanam P, Church GM (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet 29: 153–159

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Rutherford K, Parkhill J, Crook J et al. (2000) Artemis: sequence visualization and annotation. Bioinformatics 16: 944–945

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Stillman B (2001) Genomic views of genome duplication. Science 294: 2301–2304

    Article  PubMed  CAS  Google Scholar 

  • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Google Scholar 

  • The C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:2012–2018

    Google Scholar 

  • Tong AH, Evangelista M, Parsons AB et al. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364–2368

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Google Scholar 

  • Tupler R, Perini G, Green MR (2001) Expressing the human genome. Nature 409: 832–833

    Article  PubMed  CAS  Google Scholar 

  • Vidal M (2001) A biological atlas of functional maps. Cell 104: 333–339

    Article  PubMed  CAS  Google Scholar 

  • Wang Y, Liu CL, Storey JD et al. (2002) Precision and functional specificity in mRNA decay. Proc Natl Acad Sci USA 99: 5860–5865

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708–713

    Article  PubMed  CAS  Google Scholar 

  • Wood V, Bähler J (2002) How to get the best from fission yeast genome data. Comp Funct Genom 3: 282–288

    Article  CAS  Google Scholar 

  • Wood V, Rutherford KM, Ivens A et al. (2001) A re-annotation of the S. cerevisiae genome. Comp Funct Genom 2: 143–154

    Article  CAS  Google Scholar 

  • Wood V, Gwilliam R, Rajandream MA et al. (2002) The genome sequence of S. pombe. Nature 415: 871–880

    Article  PubMed  CAS  Google Scholar 

  • Young R (2000) Biomedical discovery with DNA arrays. Cell 102: 9–16

    Article  PubMed  CAS  Google Scholar 

Download references

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

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

Download citation

  • DOI: https://doi.org/10.1007/978-3-662-10360-9_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-05631-4

  • Online ISBN: 978-3-662-10360-9

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics