Periodic gene expression program of the fission yeast cell cycle

Nature Genetics

Volumn 36, Issue 8, 2004, Pages 809-817

  Rustici, Gabriella ^a   Mata, Juan ^a   Kivinen, Katja ^b   Lió, Pietro ^b   Penkett, Christopher J ^a   Burns, Gavin ^a   Hayles, Jacqueline ^c   Brazma, Alvis ^b   Nurse, Paul ^c,d   Bähler, Jürg ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^c IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^d ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COHESIN; CYCLIN DEPENDENT KINASE; DNA BINDING PROTEIN; DNA DIRECTED DNA POLYMERASE ALPHA; GLUCAN GLUCOSIDASE; HISTONE H2A; HISTONE H2B; HISTONE H3; HISTONE H4; MYOSIN II; PHOSPHOGLUCOMUTASE; RIBONUCLEOTIDE REDUCTASE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ACE2P; TRANSCRIPTION FACTOR SEP1P; UNCLASSIFIED DRUG;

ARTICLE; CELL CYCLE; CHROMOSOME CONDENSATION; CYTOKINESIS; DNA MICROARRAY; DNA REPLICATION; GENE CLUSTER; GENE EXPRESSION REGULATION; MITOSIS; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; SCHIZOSACCHAROMYCES POMBE; YEAST CELL;

CELL CYCLE; CONSERVED SEQUENCE; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES;

EUKARYOTA; SACCHAROMYCETALES; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE;

EID: 3543042493     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/ng1377     Document Type: Article

References (50)

1. Breeden, L.L. Periodic transcription: a cycle within a cycle. Curr. Biol. 13, R31-R38 (2003).
2. Spellman, P.T. et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273-3297 (1998).
3. Cho, R.J. et al. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2, 65-73 (1998).
4. Laub, M.T., McAdams, H.H., Feldblyum, T., Fraser, C.M. & Shapiro, L. Global analysis of the genetic network controlling a bacterial cell cycle. Science 290, 2144-2148 (2000).
5. Cho, R.J. et al. Transcriptional regulation and function during the human cell cycle. Nat. Genet. 27, 48-54 (2001).
6. Whitfield, M.L. et al. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol. Biol. Cell 13, 1977-2000 (2002).
7. Cooper, S. & Shedden, K. Microarray analysis of gene expression during the cell cycle. Cell Chrom. 2, 1 (2003).
8. Zhu, G. et al. Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 406, 90-94 (2000).
9. Simon, I. et al. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106, 697-708 (2001).
10. Iyer, V.R. et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533-538 (2001).
11. Horak, C.E. et al. Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev. 16, 3017-3033 (2002).
12. Lee, T.I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804 (2002).
13. Futcher, B. Transcriptional regulatory networks and the yeast cell cycle. Curr. Opin. Cell Biol. 14, 676-683 (2002).
14. Wyrick, J.J. & Young, R.A. Deciphering gene expression regulatory networks. Curr. Opin. Genet. Dev. 12, 130-136 (2002).
15. MacNeill, S.A. & Nurse, P. Cell cycle control in fission yeast. in The Molecular and Cellular Biology of the Yeast Saccharomyces: Life Cycle and Cell Biology (eds. Pringle, J.R., Broach, J., & Jones, E.W.) 697-763 (Cold Spring Harbor Press, Cold Spring Harbor, New York, USA, 1997).
16. Heckman, D.S. et al. Molecular evidence for the early colonization of land by fungi and plants. Science 293, 1129-1133 (2001).
17. Wood, V. et al. The genome sequence of Schizosaccharomyces pombe. Nature 415, 871-880 (2002).
18. Lyne, R. et al. Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data. BMC Genomics 4, 27 (2003).
19. 1 interval during the fission yeast mitotic cell cycle. EMBO J. 21, 5745-5755 (2002).
20. Watanabe, T. et al. Comprehensive isolation of meiosis-specificgenes identifies novel proteins and unusual non-coding transcripts in Schizosaccharomyces pombe. Nucl. Acids Res. 29, 2327-2337 (2001).
21. Chen, E.S., Saitoh, S., Yanagida, M. & Takahashi, K. A cell cycle-regulated GATA factor promotes centromeric localization of CENP-A in fission yeast. Mol. Cell 11, 175-187 (2003).
22. Takahashi, K., Chen, E.S. & Yanagida, M. Requirement of Mis6 centromere connector for localizing a CENP-A-like protein in fission yeast. Science 288, 2215-2219 (2000).
23. Tasto, J.J., Morrell, J.L. & Gould, K.L. An anillin homologue, Mid2p, acts during fission yeast cytokinesis to organize the septin ring and promote cell separation. J. Cell Biol. 160, 1093-1103 (2003).
24. Woollard, A., Basi, G. & Nurse, P. A novel S phase inhibitor in fission yeast. EMBO J. 15, 4603-4612 (1996).
25. Chen, D. et al. Global transcriptional responses of fission yeast to environmental stress. Mol. Biol. Cell 14, 214-229 (2003).
26. Shiozaki, K. & Russell, P. Cell-cycle control linked to extracellular environment by MAP kinase pathway in fission yeast. Nature 378, 739-743 (1995).
27. Zilahi, E., Salimova, E., Simanis, V. & Sipiczki, M. The S. pombe sep1 gene encodes a nuclear protein that is required for periodic expression of the cdc15 gene. FEBS Lett. 481, 105-108 (2000).
28. Koranda, M., Schleiffer, A., Endler, L. & Ammerer, G. Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters. Nature 406, 94-98 (2000).
29. Kumar, R., Reynolds, D.M., Shevchenko, A., Goldstone, S.D. & Dalton, S. Forkhead transcription factors, Fkh1p and Fkh2p, collaborate with Mcm1p to control transcription required for M-phase. Curr. Biol. 10, 896-906 (2000).
30. Pic, A. et al. The forkhead protein Fkh2 is a component of the yeast cell cycle transcription factor SFF. EMBO J. 19, 3750-3761 (2000).
31. Alvarez, B., Martinez, A.C., Burgering, B.M. & Carrera, A.C. Forkhead transcription factors contribute to execution of the mitotic programme in mammals. Nature 413, 744-747 (2001).
32. Martín-Cuadrado, A.B., Dueñas, E., Sipiczki, M., Vázquez de Aldana, C.R. & Del Rey, F. 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 (2003).
33. Pierrou, S., Hellqvist, M., Samuelsson, L., Enerback, S. & Carlsson, P. Cloning and characterization of seven human forkhead proteins: binding site specificity and DNA bending. EMBO J. 13, 5002-5012 (1994).
34. + gene encodes a meiosis-specific transcription factor containing a forkhead DNA-binding domain. Mol. Cell. Biol. 18, 2118-2129 (1998).
35. Mata, J., Lyne, R., Burns, G. & Bähler, J. The transcriptional program of meiosis and sporulation in fission yeast. Nat, Genet. 32, 143-147 (2002).
36. +. Nature 355, 449-453 (1992).
37. Lowndes, N.F., Johnson, A.L., Breeden, L. & Johnston, L.H. SW16 protein is required for transcription of the periodically expressed DNA synthesis genes in budding yeast. Nature 357, 505-508 (1992).
38. McInerny, C.J., Kersey, P.J., Creanor, J. & Fantes, P.A. Positive and negative roles for cdc10 in cell cycle gene expression. Nucl. Acids Res. 23, 4761-4768 (1995).
39. Wynne, J. & Treisman, R. SRF and MCM1 have related but distinct DNA binding specificities. Nucl. Acids Res. 20, 3297-3303 (1992).
40. McInerny, C.J., Partridge, J.F., Mikesell, G.E., Creemer, D.P. & Breeden, L.L. A novel Mcm1-dependent element in the SW14, CLN3, CDC6, and CDC47 promoters activates M/G1-specific transcription. Genes Dev. 11, 1277-1288 (1997).
41. 1-to-S transition in budding yeast. Mol. Cell. Biol. 21, 4140-4148 (2001).
42. Matsumoto, S. & Yanagida, M. Histone gene organization of fission yeast: a common upstream sequence. EMBO J. 4, 3531-3538 (1985).
43. Carr, A.M. et al. Analysis of a histone H2A variant from fission yeast: evidence for a role in chromosome stability. Mol. Gen. Genet. 245, 628-635 (1994).
44. Lydall, D., Ammerer, G. & Nasmyth, K. A new role for MCM1 in yeast: cell cycle regulation of SW15 transcription. Genes Dev. 5, 2405-2419 (1991).
45. McBride, H.J., Yu, Y. & Stillman, D.J. Distinct regions of the Swi5 and Ace2 transcription factors are required for specific gene activation. J. Biol. Chem. 274, 21029-21036 (1999).
46. Nasmyth, K. At the heart of the budding yeast cell cycle. Trends Genet. 12, 405-412 (1996).
47. Morgan, D.O. Cyclin-dependent kinases: engines, clocks, and microprocessors. Annu. Rev. Cell Dev. Biol. 13, 261-291 (1997).
48. Yang, I.V. et al. Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol. 3, research0062 (2002).
49. Tusher, V.G., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98, 5116-5121 (2001).
50. Vilo, J., Brazma, A., Jonassen, I., Robinson, A. & Ukkonen, E. Mining for putative regulatory elements in the yeast genome using gene expression data. Proc. Int. Conf. Intell. Syst. Mol. Biol. 8, 384-394 (2000).