Schizosaccharomyces pombe comparative genomics; from sequence to systems

Topics in Current Genetics

Volumn 15, Issue , 2006, Pages 233-285

  Wood, Valerie ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33947364411     PISSN: 16102096     EISSN: 16106970     Source Type: Book Series    
DOI: 10.1007/4735_97     Document Type: Review

References (183)

1. Aarstad K, Oyen TB (1975) On the distribution of 5s RNA cistrons on the genome of Saccharomyces cerevisiae. FEBS Lett 51:227-231
2. Akamatsu Y, Dziadkowiec D, Ikeguchi M, Shinagawa H, Iwasaki H (2003) Two different Swi5-containing protein complexes are involved in mating-type switching and recombination repair in fission yeast. Proc Natl Acad Sci 100:15770-15775
3. Alschtul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
4. Alschtul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) gapped BLAST and PSI-BLAST a new generation of database search programs. Nucleic Acids Res 1:3389-3402
5. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJ, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu ribicans. Science 297:1301-1310
6. Appelgren H, Kniola B, Ekwall K (2003) Distinct centromere domain structures with separate functions demonstrated in live fission yeast cells. J Cell Sci 116:4035-4042
7. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS (2004) UniProt: The universal protein knowledgebase. Nucleic Acids Res 32:D138-D141
8. Aravind L, Watanabe H, Lipman DJ, Koonin EV (2000) Lineage-specific gene loss and divergence of functionally linked genes in eukaryotes. Proc Natl Acad Sci 97:11319-11324
9. Asakawa H, Hayashi A, Haraguchi T, Hiraoka Y (2005) Dissociation of the Nuf2-Ndc80 complex releases centromeres from the spindle-pole body during meiotic prophase in fission yeast. Mol Biol Cell 16:2325-2538
10. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene Ontology: Tool for the unification of biology. Nat Genet 25:25-29
11. Bähler J, Wyler T, Loidl J, Kohli J (1993) Unusual nuclear structures in meiotic prophase of fission yeast: A cytological analysis. J Cell Biol 121:241-256
12. Barry JD, Ginger ML, Burton P, McCulloch R (2003) Why are parasitic contingency genes often associated with telomeres? Int J Parasitol 33:29-45
13. Barnitz JT, Cramer JH, Rownd RH, Cooley L, Soll D (1982) Arrangement of the ribosomal RNA genes in Schizosaccharomyces pombe. FEBS Lett 143:129-132
14. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR (2004) The Pfam protein families database. Nucleic Acids Res 32:D138-D141
15. Baum M, Ngan VK, Clarke L (1994) The centromeric K-type repeat and the central core are together sufficient to establish a Schizosaccharomyces pombe centromere. Mol Biol Cell 5:747-761
16. Behrens R, Hayles J, Nurse P (2000) Fission yeast retrotransposons Tf1 integration is targeted to the 5' ends of open reading frames. Nucleic Acids Res 28:4709-4716
17. Berbee ML, Taylor JW (1993) Dating the evolutionary radiations of the true fungi. Can J Bot 71:1114-1127
18. Birney E, Thompson JD, Gibson TJ (1996) PairWise and SearchWise: Finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. Nucleic Acids Res 24:2730-2739
19. Blandin G, Durrens P, Tekaia F, Aigle M, Bolotin-Fukuhara M, Bon E, Casaregola S, de Montigny J, Gaillardin C, Lepingle A, Llorente B, Malpertuy A, Neuveglise C, Ozier-Kalogeropoulos O, Perrin A, Potier S, Souciet J, Talla E, Toffano-Nioche C, Wesolowski-Louvel M, Marck C, Dujon B (2000) The genome of Saccharomyces cerevisiae revisited. FEBS Lett 487:31-36
20. Bowen NJ, Jordan IK, Epstein JA, Wood V, Levin HL (2003) Retrotransposons and their recognition of pol II promoters: A comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe. Genome Res 13:1984-1997
21. Brachat S, Dietrich FS, Voegeli S, Zhang Z, Stuart L, Lerch A, Gates K, Gaffney T, Philippsen P (2003) Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Genome Biol 4:R45
22. Brazma A, Jonassen I, Vilo J, Ukkonen E (1998) Predicting gene regulatory elements in silico on a genomic scale. Genome Res 8:1202-1215
23. Broach JR, Li YY, Feldman J, Jayaram M, Abraham J, Nasmyth KA, Hicks JB (1983) Localization and sequence analysis of yeast origins of DNA replication. Cold Spring Harb Symp Quant Biol 47 Pt2:1165-1173
24. Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, Kersey P, Mulder N, Oinn T, Maslen J, Cox A, Apweiler R (2004) The Gene Ontology Annotation (GOA) database: Sharing knowledge in Uniprot with gene ontology. Nucleic Acids Res 32:D262-66
25. Chalker DL, Sandmeyer SB (1992) Ty3 integrates within the region of RNA polymerase III transcription initiation. Genes Dev 6:117-128
26. Chen CY, Shyu AB (1995) AU-rich elements: Characterization and importance in mRNA degradation. Trends Biochem Sci 20:465-470
27. Chen D, Toone WM, Mata J, Lyne R, Burns G, Kivinen K, Brazma A, Jones N, Bähler J (2003) Global responses of fission yeast to environmental stress. Mol Biol Cell 14:214-229
28. Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D (1998) Comparison of the complete protein sets of worm and yeast: Orthology and divergence. Science 282:2022-2028
29. Chikashige Y, Kinoshita N, Nakaseko Y, Matsumoto T, Murakami S, Niwa O, Yanagida M (1989) Composite motifs and repeat symmetry in S. pombe centromeres: Direct analysis by integration of NotI restriction sites. Cell 57:739-751
30. Chikashige Y, Ding DQ, Funabiki H, Haraguchi T, Mashiko S, Yanagida M, Hiraoka Y (1994) Telomere-led premeiotic chromosome movement in fission yeast. Science 264:270-273
31. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I (1998) The transcriptional program of sporulation in budding yeast. Science 282:699-705
32. Clarke L, Baum MP (1990) Functional analysis of a centromere from fission yeast: A role for centromere-specific repeated DNA sequences. Mol Cell Biol 10:1863-1872
33. Cliften PF, Hillier LW, Fulton L, Graves T, Miner T, Gish WR, Waterston RH, Johnston M (2001) Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res 11:1175-1186
34. Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301:71-76
35. Clyne RY, Kelly TJ (1999) Genetic analysis of an ARS element from the fission yeast Schizosaccharomyces pombe. EMBO J 14:6348-6357
36. Copley R, Goodstadt L, Ponting C (2003) Eukaryotic domain evolution inferred from genome comparisons. Curr Opin Genet Dev 13:623-628
37. Dai J, Chuang R-Y, Kelly T (2005) DNA replication origins in the Schizosaccharomyces pombe genome. PNAS 102:337-342
38. Daga RR, Bolanos P, Moreno S (2003) Regulated mRNA stability of the Cdk inhibitor Rum1 links nutrient status to cell cycle progression. Curr Biol 13:2015-2024
39. Davis JC Petrov DA (2004) Preferential duplication of conserved proteins in eukaryotic genomes. PLoS 2:E55
40. Decottignies A, Sanchez-Perez I, Nurse P (2003) Schizosaccharomyces pombe essential genes: A pilot study. Genome Res 13:399-406
41. DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680-686
42. Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S, Mohr C, Pohlmann R, Luedi P, Choi S, Wing RA, Flavier A, Gaffney TD, Philippsen P (2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304:304-307
43. Doe CL, Wang G, Chow C, Fricker MD, Singh PB, Mellor EJ (1998) The fission yeast chromodomain encoding gene chp1(+) is required for chromosome segregation and shows a genetic interaction with alpha-tubulin. Nucleic Acids Res 26:4222-4229
44. Dolinski K, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Theesfeld CL, Binkley G, Lane C, Schroeder M, Sethuraman A, Dong S, Weng S, Miyasato S, Andrada R, Botstein D, Cherry JM "Saccharomyces Genome Database" http://www.yeastgenome.org/
45. Domazet-Loso T, Tautz D (2003) An evolutionary analysis of orphan genes in Drosophila. Genome Res 13:2213-2219
46. Dubey DD, Kim SM, Todorov IT, Huberman JA (1996) Large, complex modular structure of a fission yeast DNA replication origin. Curr Biol 6:467-473
47. Eddy SR (2002) Computational genomics of noncoding RNA genes. Cell 109:137-140
48. Ekwall K, Javerzat JP, Lorentz A, Schmidt H, Cranston G Allshire R (1995) The chromo-domain protein Swi6: A key component of fission yeast centromeres. Science 269:1429-1431
49. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci 95:14863-14864
50. Ettwiller LM, Rung J, Birney E (2003) Discovering novel cis-regulatory motifs using functional networks. Genome Res 13:883-895
51. Fan JB, Chikashige Y, Smith CL, Niwa O, Yanagida M, Cantor CR (1988) Construction of a Not I restriction map of the fission yeast Schizosaccharomyces pombe. Nucleic Acids Res 17:2801-2818
52. Fink GR (1987) Pseudogenes in yeast? Cell 49:5-6
53. Fitch WM (1970) Distinguishing homologs from analogous proteins. Berlin-Heidelberg-New York, Springer-Verlag
54. Fitzgerald-Hayes, Clarke L, Carbon J (1982) Nucleotide sequence comparisons and functional analysis of yeast centromere DNAs. Cell 29:235-244
55. Forsburg SL (1999) The best yeast? Trends Genet 15:340-344
56. Foury F, Roganti T, Lecrenier N, Purnelle B (1998) The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae. FEBS Lett 440:325
57. Fraser AG, Kamath RS, Zipperlen P, Martinez-Campos M, Sohrmann M, Ahringer J (2000) Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408:325-330
58. Fraser AG, Marcotte EM (2004) A probabilistic view of gene function. Nat Genet 36:559-564
59. Fraser HB, Wall DP, Hirsh AE (2003) A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol Biol 3:11
60. Fujioka Y, Kimata Y, Nomaguchi K, Watanabe K, Kohno K (2002) Identification of a novel non-structural maintenance of chromosomes (SMC) componet of the SMC5-SMC6 complex involved in DNA repair. J Biol Chem 277:21585-21591
61. Gaillardin C, Duchateau-Nguyen G, Tekaia F, Llorente B, Casaregola S, Toffano-Nioche C, Aigle M, Artiguenave F, Blandin G, Bolotin-Fukuhara M, Bon E, Brottier P, de Montigny J, Dujon B, Durrens P, Lepingle A, Malpertuy A, Neuveglise C, Ozier-Kalogeropoulos O, Potier S, Saurin W, Termier M, Wesolowski-Louvel M, Wincker P, Souciet J, Weissenbach J (2000) Genomic exploration of the hemiascomycetous yeasts: 21 Comparative functional classification of genes. FEBS Lett 487:134-149
62. Garrels JI (2002) Yeast genomic databases and the challenge of the post-genomic era. Funct Integr Genomics 2:212-237
63. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11:4241-4257
64. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG (1996) Life with 6000 genes. Science 274:546-567
65. Gomez M, Antequera F (1999) Organization of DNA replication origins in the fission yeast genome. EMBO J 18:5683-5690
66. Halme A, Bumgarner S, Styles C, Fink GR (2004) Genetic and epigenetic regulation of the FLO gene family generates cell-surface variation in yeast. Cell 116:405-415
67. Hall IM, Shankaranarayana GD, Noma K, Ayoub N, Cohen A, Grewel SI (2002) Establishment and maintenance of a heterochromatin domain. Science 297:2215-2218
68. Hansen KR, Burns G, Mata J, Volpe TA, Martienssen RA, Bähler J, Thon G (2005) Global effects on gene expression in fission yeast by silencing and RNA interference machineries. Mol Cell Biol 25:590-601
69. Heckman DS, Geiser DM, Eidell BR, Stauffer RL, Kardos NL, Hedges SB (2001) Molecular evidence for the early colonization of land by fungi and plants. Science 293:1129-1133
70. Hertz-Fowler C, Peacock CS, Wood V, Aslett M, Kerhornou A, Mooney P, Tivey A, Berriman M, Hall N, Rutherford K, Parkhill J, Ivens AC, Rajandream MA, Barrell B (2004) GeneDB: A resource for prokaryotic and eukaryotic organisms Nucleic Acids Res 32:D339-D343
71. Hirsh A, Fraser HB (2001) Protein dispensability and rate of evolution. Nature 411:1046-1049
72. Hirotsune S, Yoshida N, Chen A, Garrett L, Sugiyama F, Takahashi S, Yagami K, Wynshaw-Boris A, Yoshiki A (2003) An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423:91-96
73. Hughey R, Krogh A (1996) Hidden Markov models for sequence analysis: extensions and analysis of the basic method. Comput Appl Biosci 12:95-107
74. Ivanov IP, Gesteland RF, Matsufuji S (1998) Programmed frameshifting in the synthesis of mammalian anitzyme is +1 in mammals predominantly +1 in fission yeast, but -2 in budding yeast. RNA 4:1230-1238
75. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL (2000) The large scale organization of metabolic networks. Nature 407:651-654
76. Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411:41-42
77. Jones RH, Jones NC (1989) Mammalian cAMP-responsive element can activate transcription in yeast and binds a yeast factor(s) that resembles mammalian transcription factor ATF. Proc Natl Acad Sci 86:2176-2180
78. Jordan IK, Wolf YI, Koonin EV (2003) No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol Biol 3:1
79. Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, Gotta M, Kanapin A, Le Bot N, Moreno S, Sohrmann M, Welchman DP, Zipperlen P, Ahringer J (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421:231-237
80. Kanoh J, Ishikawa F (2003) Composition and conservation of the telomeric complex. Cell Mol Life Sci 60:2295-2302
81. Käufer NF, Potashkin J (2000) Analysis of the splicing machinery in fission yeast: A comparison with budding yeast and mammals. Nucleic Acids Res 28:3003-3010
82. Kellis M, Birren B, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in yeast Saccharomyces cerevisiae. Nature 428:617-624
83. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254
84. Keogh RS, Seoighe C, Wolfe KH (1998) Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi. Yeast 14:443-457
85. Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF (1998) Transposable elements and genome organization: A comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res 8:464-478
86. Kitajima TS, Kawashima SA, Watanabe Y (2004) The conserved kinetochore protein shugoshin protects centromeric cohesion during meiosis. Nature 427:510-517
87. Kniola B, O'Toole E, McIntosh JR, Mellone B, Allshire R, Mengarelli S, Hultenby K, Ekwall K (2001) The domain structure of centromeres is conserved from fission yeast to humans. Mol Biol Cell 12:2767-2775
88. Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. (2004) A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol 5:R7
89. Koszul R, Caburet S, Dujon B, Fischer G (2004) Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments. EMBO J 23:234-243
90. Kunin V, Pereira-Leal JB, Ouzounis CA (2004) Functional evolution of the yeast protein interaction network. Mol Biol Evol 21:1711-1716
91. Krupp G, Cherayil B, Frendewey D, Nishikawa S, Soll D (1986) Two RNA species copurify with RNase P from the fission yeast S. pombe. EMBO J 5:1697-703
92. Krylov DM, Wolf YI, Rogozin IB, Koonin EV (2003) Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res 10:2229-2235
93. Kuhn AN, Käufer NF (2003) Pre-mRNA splicing in Schizosaccharomyces pombe. Curr Genet 42:241-251
94. Kulikova T, Aldebert P, Althorpe N, Baker W, Bates K, Browne P, van den Broek A, Cochrane G, Duggan K, Eberhardt R, Faruque N, Garcia-Pastor M, Harte N, Kanz C, Leinonen R, Lin Q, Lombard V, Lopez R, Mancuso R, McHale M, Nardone F, Silventoinen V, Stoehr P, Stoesser G, Tuli MA, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R (2004) The EMBL nucleotide sequence database. Nucleic Acids Res 32:D115-D119
95. Lang BF, Cedergren R, Gray MW (1987) The mitochondrial genome of the fission yeast, Schizosaccharomyces pombe. Sequence of the large-subunit ribosomal RNA gene, comparison of potential secondary structure in fungal mitochondrial large-subunit rRNAs and evolutionary considerations. Eur J Biochem 169:527-537
96. Langkjaer RB, Cliften P, Johnston M, Piskur J (2003) Yeast genome duplication was followed by asynchronous differentiation of duplicated genes. Nature 421:848-852
97. Lespinet O, Wolf YI, Koonin EV, Aravind L (2002) The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res 12:1048-1059
98. Levin HL (1995) A novel mechanism of self-primed reverse transcription defines a new family of retroelements. Mol Cell Biol 15:3310-3317
99. Levin H, Weaver DC, Boeke JD (1990) Two related families of retrotransposons from Schizosaccharomyces pombe. Mol Cell Biol 10:6791-6798
100. Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178-2189
101. Lorentz A, Ostermann K, Fleck O (1994) Switching gene swi6, involved in repression of silent mating-type loci in fission yeast, encodes a homologue of chromatin-associated proteins from Drosophila and mammals. Gene 143:139-143
102. Lorenz A, Wells JL, Pryce DW, Novatchkova M, Eisenhaber F, McFarlane RJ, Loidl J (2004) S. pombe linear elements contain proteins related to synaptonemal complex components. J Cell Sci 117:3345-3351
103. Lowe TM, Eddy SR (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955-964
104. Lowe TM, Eddy SR (1999) A computational screen for methylation guide snoRNAs in yeast. Science 283:1168-1171
105. Lowndes NF, McInerny CJ, Johnson AL, Fantes PA, Johnston LH (1992) Control of the DNA synthesis genes in fission yeast by the cell-cycle gene cdc10+. Nature 355:449-453
106. Lum PY, Edwards S, Wright R (1996) Molecular, functional and evolutionary characterization of the gene encoding HMG-CoA reductase in the fission yeast Schizosaccharomyces pombe. Yeast 12:1107-1124
107. Malik HS, Eikbush TH (1999) Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons. J Virol 73:5186-5190
108. Mandell J, Goodrich KJ, Bähler J, Cech TR (2004) Expression of a RecQ helicase homolog affects progression through crisis in fission yeast lacking telomerase. J Biol Chem 280:5249-5257
109. Mandell JG, Bähler J, Volpe TA, Martienssen RA, Cech TR (2005) Global expression changes resulting from loss of telomeric DNA in fission yeast. Genome Biol 6:R1
110. Mao J, Appel B, Schaack J (1982) The 5S RNA genes of Schizosaccharomyces pombe. Nucleic Acids Res 10:487-500
111. Masakuto H, Huberman JA, Frattini MG, Kelly TJ (2004) DNA replication in S. pombe. In: The molecular biology of Schizosaccharomyces pombe (Egel R, Ed). Springer-Verlag Heidelberg, pp73-99
112. Mata J, Lyne R, Burns G, Bähler J (2002) The transcriptional program of meiosis and sporulation in fission yeast. Nat Genet 32:143-147
113. Mata J, Bähler J (2003) Corrlelations between gene expression and gene conservation in fission yeast. Genome Res 13:2686-2690
114. Maundrell K, Hutchison A, Shall S (1988) Sequence analysis of ARS elements in fission yeast. EMBO J 7:2203-2209
115. Maxwell PH, Coombes C, Kenny AE (2004) Ty1 mobilizes subtelomeric Y' elements in telomerase-negative Saccharomyces cerevisiae survivors. Mol Cell Biol. 24:9887-9898
116. Molnar M, Parisi S, Kakihara Y (2001) Characterization of rec7, an early meiotic recombination gene in Schizosaccharomyces pombe. Genetics 2:519-532
117. Morimyo M, Mita K, Hongo E, Higashi T, Sugaya K, Ajimura M, Yamauchi M, Tsuji S, Park W.-Y, Sasanuma S, Nohata J, Kimura T, Inoue H, Ishihara Y (1998) cDNA catalog of fission yeast (Schizosaccharomyces pombe) and its application for cloning of mammalian DNA repair gene. In: Biodefence mechanisms against environmental stress (Ozawa T, Hori T, Tatsumi K Eds), Springer Verlag Tokyo, Heidelberg, pp 115-123
118. Mott R (1997) EST_GENOME: A program to align spliced DNA sequences to unspliced genomic DNA. Comput Appl Biosci 4:477-478
119. Mundt KE, Porte J, Murray JM, Brikos C, Christensen PU, Caspari T, Hagan IM, Millar JB, Simanis V, Hofmann K, Carr AM (1999) The COP9/signalosome complex is conserved in fission yeast and has a role in S phase. Curr Biol 9:1427-1430
120. Murakami S, Matsumoto T, Niwa O, Yanagida M (1991) Structure of the fission yeast centromere cen3: Direct analysis of the reiterated inverted region. Chromosoma 101:214-221
121. Nimmo ER, Pidoux AL, Perry PE, Allshire RC (1998) Defective meiosis in telomere silencing mutants of Schizosaccharomyces pombe. Nature 392:825-828
122. Nurse P (2000) A long twentieth century of the cell cycle and beyond. Cell 100:71-78
123. Nurse P (2003) Understanding cells. Nature 424:883
124. Ohno S (1970) Evolution by gene duplication. Springer-Verlag, Berlin-Heidelberg-New York
125. Oliver SG, van der Aart QJ, Agostoni-Carbone ML, Aigle M, Alberghina L, Alexandraki D, Antoine G, Anwar R, Ballesta JP, Benit P, et al. (1992) The complete DNA sequence of yeast chromosome III. Nature 357:38-46
126. Ozier-Kalogeropoulos O, Malpertuy A, Boyer J, Tekaia F, Dujon B (1998) Random exploration of the K. lactis genome and comparison to that of S. cerevisiae. Nucleic Acids Res 26:5511-5524
127. Pagel P, Mewes H-W, Frishman D (2004) Conservation of protein-protein interactions - lessons from ascomycota. Trends Genet 20:72-76
128. Pasero P, Marilley M (1993) Size variation of rDNA clusters in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. Mol Gen Genet 236:448-452
129. Pearson W, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci 85:2444-2448
130. Piskur J (2001) Origin of the duplicated regions in the yeast genomes. Trends Genet 16:302-303
131. Pollack JR, Iyer VR (2002) Characterizing the physical genome. Nat Genet Suppl 32:515-521
132. Pradet-Balade B (2001) Translation control: Bridging the gap between genomics and proteomics? Trends Biochem Sci 26:225-229
133. Prado F, and Aguilera A (2005) Partial depletion of histone H4 increases homologous recombination-mediated genetic instability. Mol Cell Biol 24:1526-1536
134. Prince VE, Pickett (2002) Splitting pairs: The diverging fates of duplicated genes. Nat Rev Genet 3:827-837
135. Pyne S, Skiena S, Futcher B (2005) Copy correction and concerted evolution in the conservation of yeast genes. PLoS Biol, in press
136. Raghuraman MK, Winzeler EA, Collingwood D, Hunt S, Wodicka L, Conway A, Lockhart DJ, Davis RW, Brewer BJ, Fangman WL (2001) Replication dynamics of the yeast genome. Science 294:115-121
137. Remacle JE, Albrecht G, Brys R, Braus GH, Huylebroeck D (1997) Three classes of mammalian transcription activation domain stimulate transcription in Schizosaccharomyces pombe. EMBO J 16:5722-5729
138. Remm M, Storm CE, Sonnhammer EL (2001) Automatic clustering of orthologs and inparalogs from pairwise species comparisons. J Mol Biol 314:1041-1052
139. 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
140. Robyr D, Suka Y, Xenarios I, Kurdisatani SK, Wang A, Suka N, Grunstein M (2002) Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 1009:437-466
141. Rustici G, Mata J, Kivinen K, Lio P, Penkett CJ, Burns G, Hayles J, Brazma A, Nurse P, Bähler J (2004) Periodic gene expression program of the fission yeast cell cycle. Nat Genet 36:809-817
142. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B (2000) Artemis: Sequence visualization and annotation. Bioinformatics 16:944-945
143. 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
144. Scherthan H, Bähler J, Kohli J (1994) Dynamics of chromosome organization and pairing during meiotic prophase in fission yeast. J Cell Biol 127:273-285
145. Scherthan H (2001) A bouquet makes ends meet. Nat Rev Mol Cell Biol 2:621-627
146. Schroder AR, Shinn P, Chen H, Berry C, Ecker JR, Bushman F (2002) HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110:521-529
147. Segurado M, de Luis A, Antequera F (2003) Genome-wide distribution of DNA replication origins at A+T rich islands in Schizosaccharomyces pombe. EMBO reports 4:1048-1053
148. Singleton TL, Levin HL (2002) A long terminal repeat retrotransposon of fission yeast has strong preferences for specific sites of insertion. Eukaryot Cell 1:44-55
149. Sipiczki M (2001) Where does fission yeast sit on the tree of life? Genome Biol 1:1011.1-1011.4
150. Smith CL, Matsumoto T, Niwa O, Klco S, Fan JB, Yanagida M, Cantor CR (1987) An electrophoretic karyotype for Schizosaccharomyces pombe by pulsed field gel electrophoresis. Nucleic Acids Res 15:4481-4491
151. Sonnhammer EL, Eddy SR, Durbin R (1997) Pfam: A comprehensive database of protein domain families based on seed alignments Proteins 3:405-420
152. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B (1998) Comprehensive identification of cell-cycle regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9:3273-3297
153. Sunnerhagen P (2002) Prospects for functional genomics in Schizosaccharomyces pombe. Curr Genet 42:73-84
154. Takahashi K, Murakami S, Chikashige Y, Funabiki H, Niwa O, Yanagida M (1992) A low copy number central sequence with strict symmetry and unusual chromatin structure in the fission yeast centromere. Mol Biol Cell 3:819-835
155. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on global families. Science 278:631-637
156. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA (2003) The COG database: An updated version includes eukaryotes. BMC Bioinformatics 4:41
157. Teichmann SA (2002) The constraints protein-protein interactions place on sequence divergence. J Mol Biol 324:399-407
158. The C. elegans sequencing consortium (1998) Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282:2012-2018
159. The Gene Ontology Consortium (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32:D258-D261
160. Theis JF, Newlon CS (1997) The ARS309 chromosomal replicator of Schizosaccharomyces cerevisiae depends on an exceptional ARS consensus sequence. Proc Natl Acad Sci USA 94:10786-10791
161. Theis JF, Newlon CS (2001) Two compound replication origins in Saccharomyces cerevisiae contain redundant origin complex binding sites. Mol Cell Biol 21:2790-2801
162. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice. Nucl Acids Res 22:4673-4680
163. van Driel R (2003) The eukaryotic genome: A system regulated at different hierarchical levels. J Cell Sci 116:4067-4075
164. Villeneuve AM, Hillers KJ (2001) Whence meiosis? Cell 106:647-650
165. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA (2002) Regulation of heterochromatin silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833-1837
166. Volpe T, Schramke V, Hamilton, White SA, Teng G, Martienssen RA, Allshire RC (2003) RNA interference is required for normal centromere function in fission yeast. Chromosome Res 11:137-146
167. + 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
168. Watanabe T, Miyashita K, Saito TT (2001) Comprehensive isolation of meiosis-specific genes identifies novel proteins and unusual non-coding transcripts in Schizosaccharomyces pombe. Nucleic Acids Res 29:327-337
169. 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
170. Webb CJ, Wise JA (2004) The splicing factor U2AF small subunit is functionally conserved between fission yeast and humans. Mol Cell Biol 10:4229-4240
171. Wood V, Rutherford K, Ivens A, Rajandream M-A, Barrell B (2001) A re-annotation of the Saccharomyces cerevisiae genome. Comp Funct Genom 2:143-154
172. Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A, Davis P, Feltwell T, Fraser A, Gentles S, Goble A, Hamlin N, Harris D, Hidalgo J, Hodgson G, Holroyd S, Hornsby T, Howarth S, Huckle EJ, Hunt S, Jagels K, James K, Jones L, Jones M, Leather S, McDonald S, McLean J, Mooney P, Moule S, Mungall K, Murphy L, Niblett D, Odell C, Oliver K, O'Neil S, Pearson D, Quail MA, Rabbinowitsch E, Rutherford K, Rutter S, Saunders D, Seeger K, Sharp S, Skelton J, Simmonds M, Squares R, Squares S, Stevens K, Taylor K, Taylor RG, Tivey A, Walsh S, Warren T, Whitehead S, Woodward J, Volckaert G, Aert R, Robben J, Grymonprez B, Weltjens I, Vanstreels E, Rieger M, Schafer M, Muller-Auer S, Gabel C, Fuchs M, Fritzc C, Holzer E, Moestl D, Hilbert H, Borzym K, Langer I, Beck A, Lehrach H, Reinhardt R, Pohl TM, Eger P, Zimmermann W, Wedler H, Wambutt R, Purnelle B, Goffeau A, Cadieu E, Dreano S, Gloux S, et al. (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415:871-880
173. Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713
174. Wolfe K (2004) Evolutionary genomics: Yeast accelerate beyond BLAST. Curr Biol 14: R392-R394
175. Wong S, Butler G, Wolfe KH (2002) Gene order evolution and paleopolyploidy in hemiascomycete yeasts. Proc Natl Acad Sci 14:9272-9277
176. Wyrick JJ, Aparicio JG, Chen T, Barnett JD, Jennings EG, Young RA, Bell SP, Aparicio OM (2001) Genome-wide distribution of ORC and NCN proteins in S. cerevisiae: High resolution mapping of replication origins. Science 294:2357-2360
177. Yamanda M, Hayatsu N, Matsuura A, Ishikawa F (1998) Y'-Help1, a DNA helicase encoded by the yeast subtelomeric Y' element, is induced in survivors defective for telomerase. J Biol Chem 273:33360-33366
178. Yanagida M (2002) The model unicellular eukaryote, Schizosaccharomyces pombe. Genome Biol 3:COMMENT2003.1-2003.4
179. Yieh L, Kassavetis G, Geiduscheck EP, Sandmeyer SB (2000) The Brf and TATA-binding proteins subunits of the RNA polymerase III transcription factor IIIB mediate position specific integration of the gypsy-like
180. Young JA, Schreckhise RW, Steiner WW, Smith GR (2002) Meiotic recombination remote from prominent break sites in S. pombe. Mol Cell 9:253-263
181. Young JA, Hyppa RW, Smith GR (2004) Swi5 acts in meiotic DNA joint molecule formation in Schizosaccharomyces pombe. Genetics 167:593-605
182. Zdobnov EM, von Mering C, Letunic I, Bork P (2002) Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 298:149-159
183. Zhu C, Karplus K, Grate L, Coffino P (2000) A homolog of mammalian antizyme is present in fission yeast Scizosaccharomyces pombe but not detected in budding yeast Saccharomyces cerevisiae. Bioinformatics 16:478-481