Identification of cell cycle-regulated genes in fission yeast

Molecular Biology of the Cell

Volumn 16, Issue 3, 2005, Pages 1026-1042

  Peng, Xu ^a   Karuturi, R Krishna Murthy ^a   Miller, Lance D ^a   Lin, Kui ^a,f   Jia, Yonghui ^a   Kondu, Pinar ^b   Wang, Long ^a   Wong, Lim Soon ^c   Liu, Edison T ^a   Balasubramanian, Mohan K ^d,e   Liu, Jianhua ^a,e  

^a GENOME INSTITUTE OF SINGAPORE   (Singapore)

^b BIOINFORMATICS INSTITUTE   (Singapore)

^c INSTITUTE FOR INFOCOMM RESEARCH   (Singapore)

^d TEMASEK LIFE SCIENCES LABORATORY   (Singapore)

^e NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^f BEIJING NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; OLIGONUCLEOTIDE;

ARTICLE; CELL CULTURE; CELL CYCLE; CELL MUTANT; DNA MICROARRAY; DNA SYNTHESIS; FUNGAL GENE; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; GENOME; MITOSIS INHIBITION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MOTIF; SCHIZOSACCHAROMYCES POMBE; WILD TYPE; YEAST;

ALGORITHMS; AMINO ACID MOTIFS; CELL CYCLE; CELL CYCLE PROTEINS; CELL NUCLEUS; CELL SEPARATION; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DNA; DNA, COMPLEMENTARY; FLOW CYTOMETRY; FUNGAL PROTEINS; G1 PHASE; G2 PHASE; GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; GENOTYPE; INTERNET; MODELS, STATISTICAL; NORMAL DISTRIBUTION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS (GENETICS); RAS-GRF1; RNA, MESSENGER; S PHASE; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES; SPECIES SPECIFICITY; TEMPERATURE; TRANSCRIPTION, GENETIC;

SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES; SCHIZOSACCHAROMYCES POMBE;

EID: 20044366888     PISSN: 10591524     EISSN: None     Source Type: Journal    
DOI: 10.1091/mbc.E04-04-0299     Document Type: Article

References (78)

1. Alemany, V., Sanchez-Piris, M., Bachs, O., and Aligue, R. (2002). Cmk2, a novel serine/threonine kinase in fission yeast. FEBS Lett. 524, 79-86.
2. 1interval during the fission yeast mitotic cell cycle. EMBO J. 21, 5745-5755.
3. Ayte, J., Schweitzer, C., Zarzov, P., Nurse, P., and DeCaprio, J. A. (2001). Feedback regulation of the MBF transcription factor by cyclin Cig2. Nat. Cell Biol. 3, 1043-1050.
4. Bähler, J., Wu, J.-Q., Longtine, M. S., Shah, N. G., McKenzie, A., Steever, A. B., Wach, A., Philippsen, P., and Pringle, J. R. (1998). Heterologous modules for efficient and versatile PCR-based gene targeting in Schizosaccharomyces pombe. Yeast 14, 943-951.
5. rum1CDK inhibitor. EMBO J. 17, 482-497.
6. Birkenbihl, R. P., and Subramani, S. (1995). The rad21gene product of Schizosaccharomyces pombe is a nuclear, cell cycle-regulated phosphoprotein. J. Biol. Chem. 270, 7703-7711.
7. Borgne, A., Murakarni, H., Ayte, J., and Nurse, P. (2002). The G1/S cyclin Cig2p during meiosis in fission yeast. Mol. Biol. Cell 13, 2080-2090.
8. Brown, G. W., and Kelly, T. J. (1999). Cell cycle regulation of Dfp1, an activator of the Hsk1 protein kinase. Proc. Natl. Acad. Sci. USA 96, 8443-8448.
9. Caligiuri, M., and Beach, D. (1993). Sct1 functions in partnership with Cdc10 in a transcription complex that activates cell cycle START and inhibits differentiation. Cell 72, 607-619.
10. Carr, A. M., Dorrington, S. M., Hindley, J., Phear, G. A., Aves, S. J., and Nurse, P. (1994). Analysis of a histone H2A variant from fission yeast: evidence for a role in chromosome stability. Mol. Gen. Genet. 245, 628-635.
11. Carter, M. G., et al. (2003). In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling. Genome Res. 13, 1011-1021.
12. Chen, E. S., Saitoh, S., Yanagida, M., and Takahashi, K. (2003). A cell cycle-regulated GATA factor promotes centromeric localization of CENP-A in fission yeast. Mol. Cell. 11, 175-187.
13. Cho, R. J., et al.(1998). A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell. 2, 65-73.
14. Cho, R. J., Huang, M., Campbell, M. J., Dong, H., Steinmetz, L., Sapinoso, L., Hampton, G., Elledge, S. J., Davis, R. W., and Lockhart, D. J. (2001). Transcriptional regulation and function during the human cell cycle. Nat. Genet. 27, 48-54.
15. Choe, J., Schuster, T., and Grunstein, M. (1985). Organization, primary structure, and evolution of histone H2A and H2B genes of the fission yeast Schizosaccharomyces pombe. Mol. Cell. Biol. 5, 3261-3269.
16. Christensen, P. U., Bentley, N. J., Martinho, R. G., Nielsen, O., and Carr, A. M. (2000). Mik1 levels accumulate in S phase and may mediate an intrinsic link between S phase and mitosis. Proc. Natl. Acad. Sci. USA 97, 2579-2584.
17. Ducommun, B., Draetta, G., Young, P., and Beach, D. (1990). Fission yeast cdc25is a cell-cycle regulated protein. Biochem. Biophys. Res. Commun. 167, 301-309.
18. Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863-14868.
19. Fankhauser, C., Reymond, A., Cerutti, L., Utzig, S., Hofmann, K., and Simanis, V. (1995). The S. pombe cdc15gene is a key element in the reorganization of F-actin at mitosis. Cell 82, 435-444.
20. +gene encodes a member of the MCM family of replication proteins. J. Cell Sci. 107, 2779-2788.
21. Futcher, B. (2000). Microarrays and cell cycle transcription in yeast. Curr. Opin. Cell Biol. 12, 710-715.
22. Hagan, I. M., and Hyams, J. S. (1988). The use of cell division cycle mutants to investigate the control of microtubule distribution in the fission yeast Schizosaccharomyces pombe. J. Cell Sci. 89, 343-357.
23. +expression in fission yeast. Mol. Gen. Genet. 252, 284-291.
24. Heckman, D. S., Geiser, D. M., Eidell, B. R., Stauffer, R. L., Kardos, N. L., and Hedges, S. B. (2001). Molecular evidence for the early colonization of land by fungi and plants. Science 293, 1129-1133.
25. Hofmann, J.F.X., and Beach, D. (1994). cdt1 is an essential target of the Cdc10/Sct1 transcription factor: requirement for DNA replication and inhibition of mitosis. EMBO J. 13, 425-434.
26. Kane, M. D., Jatkoe, T. A., Stumpf, C. R., Lu, J., Thomas, J. D., and Madore, S. J. (2000). Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res. 28, 4552-4557.
27. Karuturi, K. M., and Liu, J. (2004). Improved Fourier Transform method for unsupervised cell-cycle regulated gene prediction. In: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference, Stanford, CA (http://conferences.computer.org/bioinformatics/CSB2004/Program4.htm).
28. +gene product couples S phase to START and mitosis. Cell 74, 371-382.
29. +, a UV-inducible gene from Schizosaccharomyces pombe. Environ. Mol. Mutagen 30, 72-81.
30. Krien, M.J.E., West, R. R., John, U. P., Koniaras, K., McIntosh, J. R., and O'Connell, M. J. (2002). The fission yeast NIMA kinase Fin1p is required for spindle function and nuclear envelope integrity. EMBO J. 21, 1713-1722.
31. Lin, K., Liu, J., Miller, D. L., and Wong, L. (2004). Genome-wide cDNA oligo design and its applications in Schizosaccharomyces pombe. In: The Practical Bioinformatidan, ed. L. Wong, Singapore: World Scientific Publishing, 347-358.
32. +. Nature 355, 449-453.
33. Lydall, D., Ammerer, G., and Nasmyth, K. (1991). A new role for MCM1 in yeast: cell cycle regulation of SW15transcription. Genes Dev. 5, 2405-2419.
34. MacNeill, S. A., and Fantes, P. A. (1997). Genetic and physiological analysis of DNA replication in fission yeast. Methods Enzymol. 283, 440-459.
35. MacNeill, S. A., and Nurse, P. (1997). Cell cycle control in fission yeast. In: The Molecular and Cellular Biology of the Yeast Saccharomyces. Cell Cycle and Cell Biology, ed. J. R. Pringle, J. R. Broach, and E. W. Jones, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 697-763.
36. +transcription in fission yeast. Mol. Gen. Genomics 269, 765-775.
37. Martin-Cuadrado, A. B., Dueñas, E., Sipiczki, M., Vázquez de Aldana, C. R., and del Rey, F. (2003). The endo-β-1,3-glucanase eng1p is required for dissolution of the primary septum during cell separation in Schizosaccharomyces pombe. J. Cell Sci. 116, 1689-1698.
38. Matsumoto, S., and Yanagida, M. (1985). Histone gene organization of fission yeast: a common upstream sequence. EMBO J. 4, 3531-3538.
39. McInerny, C. J., Kersey, P. J., Creanor, J., and Fantes, P. A. (1995). Positive and negative roles for cdc10in cell cycle gene expression. Nucleic Acids Res. 23, 4761-4768.
40. Mitchison, J. M. (1970). Physiological and cytological methods for Schizosacchromyces pombe. Methods Cell Physiol. 4, 131-165.
41. Mitchison, J. M., Creanor, J., and Novak, B. (1991). Coordination of growth and division during the cell cycle of fission yeast. Cold Spring Harbor Symp. Quant. Biol. 56, 557-565.
42. +/SWI4 family, controls the "start" of mitotic and meiotic cycles in fission yeast. EMBO J. 13, 1873-1880.
43. Muzi-Falconi, M., and Kelly, T. J. (1995). Orp1, a member of the Cdc18/Cdc6 family of S-phase regulators, is homologous to a component of the origin recognition complex. Proc. Natl. Acad. Sci. USA 92, 12475-12479.
44. Nakashima, N., Tanaka, K., Sturm, S., and Okayama, H. (1995). Fission yeast Rep2 is a putative transcriptional activator subunit for the cell cycle "start" function of Res2-Cdc10. EMBO J. 14, 4794-4802.
45. Nasmyth, K., Nurse, P., and Fraser, R.S.S. (1979). The effect of cell mass on the cell cycle timing and duration of S-phase in fission yeast. J. Cell Sci. 39, 215-233.
46. +G1-S transcription regulates mitotic entry in fission yeast. FEBS Lett. 503, 131-134.
47. Nurse, P. (1990). Universal control mechanism regulating onset of M-phase. Nature 344, 503-508.
48. Obara-Ishihara, T., and Okayama, H. (1994). A B-type cyclin negatively regulates conjugation via interacting with cell cycle 'start' genes in fission yeast. EMBO J. 13, 1863-1872.
49. +essential for a midmitotic transition encodes a leucine-rich repeat protein that positively modulates protein phosphatase-1. Cell 64, 149-157.
50. Plochocka-Zulinska, D., Rasmussen, G., and Rasmussen, C. (1995). Regulation of calcineurin gene expression in Schizosaccharomyces pombe. Dependence on the ste11 transcription factor. J. Biol. Chem. 270, 24794-24799.
51. Rasmussen, C. D. (2000). Cloning of a calmodulin kinase 1 homologue from Schizosaccharomyces pombe. J. Biol. Chem. 275, 685-690.
52. cdc10function. Mol. Gen. Genet. 234, 449-456.
53. +encodes a transcription-factor homologue of the HNF-3/forkhead DNA-binding-domain family in Schizosaccharomyces pombe. Gene 202, 1-5.
54. +forkhead transcription factor homologue is not lethal but causes hyphal growth in Schizosaccharomyces pombe. Biochem. Biophys. Res. Commun. 263, 465-474.
55. Rifkin, S. A., and Kim, J. (2002). Geometry of gene expression dynamics. Bioinformatics 18, 1176-1183.
56. Robinow, C. F. (1977). The number of chromosomes in Schizosaccharomyces pombe: light microscopy of stained preparations. Genetics 87, 491-497.
57. Rowley, R., Hudson, J., and Young, P. G. (1992). The wee1protein kinase is required for radiation-induced mitotic delay. Nature 356, 353-355.
58. +functions as an inducer in the mitotic control of fission yeast. Cell 45, 145-153.
59. Rustici, G., Mata, J., Kivinen, K., Lio, P., Penkett, C. J., Burns, G., Hayles, J., Brazma, A., Nurse, P., and Bähler, J. (2004). Periodic gene expression program of the fission yeast cell cycle. Nat. Genet. 36, 809-817.
60. Samuel, J. M., Fournier, N., Simanis, V., and Millar, J.B.A. (2000). spo12 is a multicopy suppressor of mcs3that is periodically expressed in fission yeast mitosis. Mol. Gen. Genet. 264, 306-316.
61. Sellers, J. W., Vincent, A. C., and Struhl, K. (1990). Mutations that define the optimal half-site for binding yeast GCN4 activator protein and identify an ATF/CREB-like repressor that recognizes similar DNA sites. Mol Cell. Biol. 10, 5077-5086.
62. Simon, I., et al. (2001). Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106, 697-708.
63. Spellman, P. T., Sherlock, G., Zhang, M. Q., Iyer, V. R., Anders, K., Eisen, M. B., Brown, P. O., Botstein, D., and Futcher, B. (1998). Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273-3297.
64. Sugiyama, A., Tanaka, K., Okazaki, K., Nojima, H., and Okayama, H. (1994). A zinc finger protein controls the onset of premeiotic DNA synthesis of fission yeast in a Mei2-independent cascade. EMBO J. 13, 1881-1887.
65. Takahashi, K., Chen, E. S., and Yanagida, M. (2000). Requirement of Mis6 centromere connector for localizing a CENP-A-like protein in fission yeast. Science 288, 2215-2219.
66. +, encoding a regulatory subunit for Hsk1 kinase, plays essential roles in S-phase initiation as well as in S-phase checkpoint control and recovery from DNA damage. Mol. Cell. Biol. 19, 5535-5547.
67. + gene encodes an essential 5′ to 3′ DNA helicase required for the completion of S-phase. Nucleic Acids Res. 30, 4728-4739.
68. Tanaka, K., and Russell, P. (2001). Mrc1 channels the DNA replication arrest signal to checkpoint kinase Cds1. Nat. Cell Biol. 3, 966-972.
69. Tang, H., and Lewontin, R. C. (1999). Locating regions of differential variability in DNA and protein sequences. Genetics 153, 485-495.
70. Tournier, S., and Millar, J.B.A. (2000). A role for the START gene-specific transcription factor complex in the inactivation of cyclin B and Cut2 destruction. Mol. Biol. Cell 11, 3411-3424.
71. +in MCB gene transcription at the mitotic G1-S boundary in fission yeast. Curr. Genet. 40, 251-259.
72. Whitehall, S., Stacey, P., Dawson, K., and Jones, N. (1999). Cell cycle-regulated transcription in fission yeast: Cdc10-Res protein interactions during the cell cycle and domains required for regulated transcription. Mol. Biol. Cell 10, 3705-3715.
73. Whitfield, M. L., et al. (2002). Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol. Biol. Cell 13, 1977-2000.
74. Wood, V., et al.(2002). The genome sequence of Schizosaccharomyces pombe. Nature 415, 871-880.
75. +, a homolog of CDC20/p55CDC/Fizzy. J. Cell Sci. 113, 3989-3999.
76. 1-specific promoter of mitotic cyclin B degradation. EMBO J. 19, 3968-3977.
77. cdc10, is required for meiosis in the fission yeast Schizosaccharomyces pombe. Genes Dev. 8, 885-898.
78. Zilahi, E., Salimova, E., Simanis, V., and Sipiczki, M. (2000). The S. pombe sep1gene encodes a nuclear protein that is required for periodic expression of the cdc15 gene. FEBS Lett. 481, 105-108.