Cell cycle goes global

Current Opinion in Cell Biology

Volumn 16, Issue 6, 2004, Pages 602-613

  Tyers, Mike ^a  

^a MOUNT SINAI HOSPITAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE; DNA;

AUTOMATION; CELL CYCLE; CELL DIVISION; CELL STRUCTURE; DNA REPLICATION; ENZYME SUBSTRATE; GENE CONTROL; GENE FUNCTION; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENOMICS; HUMAN; MATHEMATICAL MODEL; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA INTERACTION; PROTEOMICS; REVIEW; SIGNAL TRANSDUCTION; SISTER CHROMATID;

ANIMALS; CELL CYCLE; CELL DIVISION; COMPUTATIONAL BIOLOGY; DNA REPLICATION; GENOMICS; HUMANS; MODELS, BIOLOGICAL; RNA INTERFERENCE; TRANSCRIPTION, GENETIC;

NEGIBACTERIA;

EID: 7744220830     PISSN: 09550674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ceb.2004.09.013     Document Type: Review

References (111)

1. A.W. Murray, and D. Marks Can sequencing shed light on cell cycling? Nature 409 2001 844 846
2. G.D. Bader, A. Heilbut, B. Andrews, M. Tyers, T. Hughes, and C. Boone Functional genomics and proteomics: charting a multidimensional map of the yeast cell Trends Cell Biol 13 2003 344 356
3. S.I. Reed Ratchets and clocks: the cell cycle, ubiquitylation and protein turnover Nat Rev Mol Cell Biol 4 2003 855 864
4. G. Giaever, A.M. Chu, L. Ni, C. Connelly, L. Riles, S. Veronneau, S. Dow, A. Lucau-Danila, K. Anderson, and B. Andre Functional profiling of the Saccharomyces cerevisiae genome Nature 418 2002 387 391
5. A.H. Tong, M. Evangelista, A.B. Parsons, H. Xu, G.D. Bader, N. Page, M. Robinson, S. Raghibizadeh, C.W. Hogue, and H. Bussey Systematic genetic analysis with ordered arrays of yeast deletion mutants Science 294 2001 2364 2368
6. S.L. Ooi, D.D. Shoemaker, and J.D. Boeke DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray Nat Genet 35 2003 277 286 SLAM is developed as a method and used to identify novel genetic interactions with the SGS1 and SRS2 helicase genes.
7. A.H. Tong, G. Lesage, G.D. Bader, H. Ding, H. Xu, X. Xin, J. Young, G.F. Berriz, R.L. Brost, and M. Chang Global mapping of the yeast genetic interaction network Science 303 2004 808 813 The SGA method for systematic mapping of synthetic lethal interactions in yeast is used to provide a snapshot of the global genetic interaction network. Data from 132 SGA screens spanning query genes with functions in cell polarity, the cell wall, chromosome segregation, and the DNA replication and repair pathways is reported.
8. A.E. Carpenter, and D.M. Sabatini Systematic genome-wide screens of gene function Nat Rev Genet 5 2004 11 22
9. W.K. Huh, J.V. Falvo, L.C. Gerke, A.S. Carroll, R.W. Howson, J.S. Weissman, and E.K. O'Shea Global analysis of protein localization in budding yeast Nature 425 2003 686 691
10. S. Ghaemmaghami, W.K. Huh, K. Bower, R.W. Howson, A. Belle, N. Dephoure, E.K. O'Shea, and J.S. Weissman Global analysis of protein expression in yeast Nature 425 2003 737 741
11. M. Tyers, and M. Mann From genomics to proteomics Nature 422 2003 193 197
12. R. Aebersold, and M. Mann Mass spectrometry-based proteomics Nature 422 2003 198 207
13. J. Reboul, P. Vaglio, J.F. Rual, P. Lamesch, M. Martinez, C.M. Armstrong, S. Li, L. Jacotot, N. Bertin, and R. Janky C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression Nat Genet 34 2003 35 41
14. L. Giot, J.S. Bader, C. Brouwer, A. Chaudhuri, B. Kuang, Y. Li, Y.L. Hao, C.E. Ooi, B. Godwin, and E. Vitols A protein interaction map of Drosophila melanogaster Science 302 2003 1727 1736 The first systematic protein interaction map of a metazoan, based on 20405 candidate interactions between 7048 proteins. A high confidence map of 4780 interactions between 4679 proteins is developed by statistical criteria.
15. S. Li, C.M. Armstrong, N. Bertin, H. Ge, S. Milstein, M. Boxem, P.O. Vidalain, J.D. Han, A. Chesneau, and T. Hao A map of the interactome network of the metazoan C. elegans Science 303 2004 540 543 This systematic analysis of protein interactions by directed two-hybrid tests identifies >4,000 interactions. An overall map of 5,500 interactions is built from additional literature and predicted interactions.
16. H. Zhu, M. Bilgin, and M. Snyder Proteomics Annu Rev Biochem 72 2003 783 812
17. B. Futcher Transcriptional regulatory networks and the yeast cell cycle Curr Opin Cell Biol 14 2002 676 683 An excellent overview of issues still pertinent to the dissection of transcriptional regulatory networks.
18. T.I. Lee, N.J. Rinaldi, F. Robert, D.T. Odom, Z. Bar-Joseph, G.K. Gerber, N.M. Hannett, C.T. Harbison, C.M. Thompson, and I. Simon Transcriptional regulatory networks in Saccharomyces cerevisiae Science 298 2002 799 804
19. C.E. Horak, N.M. Luscombe, J. Qian, P. Bertone, S. Piccirrillo, M. Gerstein, and M. Snyder Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae Genes Dev 16 2002 3017 3033
20. •], alignment of promoter regions from several closely related yeast species allows the identification of conserved regulatory motifs.
21. •].
22. Chua G, Robinson MD, Morris Q, Hughes T: Transcriptional networks: reverse engineering gene regulation on a global scale. Curr Opin Microbiol 2004, in press.
23. M.T. Laub, H.H. McAdams, T. Feldblyum, C.M. Fraser, and L. Shapiro Global analysis of the genetic network controlling a bacterial cell cycle Science 290 2000 2144 2148
24. G. Rustici, J. Mata, K. Kivinen, P. Lio, C.J. Penkett, G. Burns, J. Hayles, A. Brazma, P. Nurse, and J. Bahler Periodic gene expression program of the fission yeast cell cycle Nat Genet 36 2004 809 817 Comprehensive analysis of expression profiles in synchronous cultures of fission yeast reveals that only 136 genes are periodically expressed, compared to some 800 in budding yeast; that periodic transcription occurs over only a small window of the cell cycle; and that there is no evidence for an overall circuit of transcriptional control. ∼40 periodically expressed genes conserved between the two yeasts may form the core transcriptional backbone of the mitotic cell cycle.
25. R.J. Cho, M. Huang, M.J. Campbell, H. Dong, L. Steinmetz, L. Sapinoso, G. Hampton, S.J. Elledge, R.W. Davis, and D.J. Lockhart Transcriptional regulation and function during the human cell cycle Nat Genet 27 2001 48 54
26. M.L. Whitfield, G. Sherlock, A.J. Saldanha, J.I. Murray, C.A. Ball, K.E. Alexander, J.C. Matese, C.M. Perou, M.M. Hurt, and P.O. Brown Identification of genes periodically expressed in the human cell cycle and their expression in tumors Mol Biol Cell 13 2002 1977 2000
27. K. Vandepoele, J. Raes, L. De Veylder, P. Rouze, S. Rombauts, and D. Inze Genome-wide analysis of core cell cycle genes in Arabidopsis Plant Cell 14 2002 903 916
28. M.T. Laub, S.L. Chen, L. Shapiro, and H.H. McAdams Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle Proc Natl Acad Sci USA 99 2002 4632 4637
29. J. Holtzendorff, D. Hung, P. Brende, A. Reisenauer, P.H. Viollier, H.H. McAdams, and L. Shapiro Oscillating global regulators control the genetic circuit driving a bacterial cell cycle Science 304 2004 983 987 A detailed analysis of the circuits that underlie a bacterial cell cycle.
30. •] report the identification of many new E2F target genes by ChIP-chip technology.
31. •].
32. J.L. Lavrrar, and P.J. Farnham The use of transient chromatin immunoprecipitation assays to test models for E2F1-specific transcriptional activation J Biol Chem 2004
33. C.S. Newlon, and J.F. Theis DNA replication joins the revolution: whole-genome views of DNA replication in budding yeast Bioessays 24 2002 300 304
34. D. Schubeler, D. Scalzo, C. Kooperberg, B. van Steensel, J. Delrow, and M. Groudine Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing Nat Genet 32 2002 438 442
35. K. Woodfine, H. Fiegler, D.M. Beare, J.E. Collins, O.T. McCann, B.D. Young, S. Debernardi, R. Mott, I. Dunham, and N.P. Carter Replication timing of the human genome Hum Mol Genet 13 2004 191 202
36. Y. Katou, Y. Kanoh, M. Bando, H. Noguchi, H. Tanaka, T. Ashikari, K. Sugimoto, and K. Shirahige S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex Nature 424 2003 1078 1083 High-density oligonucleotide arrays that cover chromosome VI at 300-bp intervals enable fine-scale resolution of replication fork progression under conditions of replication stress and in checkpoint mutants.
37. 1 Mol Cell 9 2002 1067 1078 Visualization of single DNA fibres reveals a much greater inter-origin spacing in cells that are unable to fully inactivate CDK activity at the end of mitosis.
38. C.J. Merrick, D. Jackson, and J.F. Diffley Visualization of altered replication dynamics after DNA damage in human cells J Biol Chem 279 2004 20067 20075
39. F. Uhlmann The mechanism of sister chromatid cohesion Exp Cell Res 296 2004 80 85
40. •], ChIP-chip analysis demonstrates the concentration of cohesin at sites of convergent transcription in yeast.
41. •].
42. S.A. Weber, J.L. Gerton, J.E. Polancic, J.L. DeRisi, D. Koshland, and P.C. Megee The kinetochore is an enhancer of pericentric cohesin binding PLoS Biol 2 2004 E260
43. cdc2: in vivo veritas? Cell 61 1990 549 551
44. Y. Ho, A. Gruhler, A. Heilbut, G.D. Bader, L. Moore, S.L. Adams, A. Millar, P. Taylor, K. Bennett, and K. Boutilier Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 415 2002 180 183
45. V. Archambault, E.J. Chang, B.J. Drapkin, F.R. Cross, B.T. Chait, and M.P. Rout Targeted proteomic study of the cyclin-cCDK module Mol Cell 14 2004 699 711 Sensitive mass spectrometric analysis of complexes nucleated around each main cyclin-Cdc28 complex is used to identify novel substrates and to map many phosphorylation sites.
46. S.B. Ficarro, M.L. McCleland, P.T. Stukenberg, D.J. Burke, M.M. Ross, J. Shabanowitz, D.F. Hunt, and F.M. White Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae Nat Biotechnol 20 2002 301 305
47. A.C. Bishop, J.A. Ubersax, D.T. Petsch, D.P. Matheos, N.S. Gray, J. Blethrow, E. Shimizu, J.Z. Tsien, P.G. Schultz, and M.D. Rose A chemical switch for inhibitor-sensitive alleles of any protein kinase Nature 407 2000 395 401
48. J.A. Ubersax, E.L. Woodbury, P.N. Quang, M. Paraz, J.D. Blethrow, K. Shah, K.M. Shokat, and D.O. Morgan Targets of the cyclin-dependent kinase Cdk1 Nature 425 2003 859 864 A combination of sophisticated analog-sensitive kinase biochemistry and brute force screen identifies some 200 new CDK substrates.
49. H. Zhu, J.F. Klemic, S. Chang, P. Bertone, A. Casamayor, K.G. Klemic, D. Smith, M. Gerstein, M.A. Reed, and M. Snyder Analysis of yeast protein kinases using protein chips Nat Genet 26 2000 283 289
50. A.E. Elia, L.C. Cantley, and M.B. Yaffe Proteomic screen finds pSer/pThr-binding domain localizing Plk1 to mitotic substrates Science 299 2003 1228 1231
51. S.E. Meek, W.S. Lane, and H. Piwnica-Worms Comprehensive proteomic analysis of interphase and mitotic 14-3-3-binding proteins J Biol Chem 279 2004 32046 32054
52. J. Peng, D. Schwartz, J.E. Elias, C.C. Thoreen, D. Cheng, G. Marsischky, J. Roelofs, D. Finley, and S.P. Gygi A proteomics approach to understanding protein ubiquitination Nat Biotechnol 21 2003 921 926
53. I.M. Cheeseman, S. Anderson, M. Jwa, E.M. Green, J. Kang, J.R. Yates III, C.S. Chan, D.G. Drubin, and G. Barnes Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p Cell 111 2002 163 172 The first systematic interrogation of kinetochore complexes by affinity purification and mass spectrometric analysis of 28 kinetochore subunits. Phosphorylation site mapping and mutational analysis demonstrate regulation of the microtubule binding protein Dam1 by the kinase Ipl1.
54. P. De Wulf, A.D. McAinsh, and P.K. Sorger Hierarchical assembly of the budding yeast kinetochore from multiple subcomplexes Genes Dev 17 2003 2902 2921 The interactions between 31 centromere-associated proteins are assessed by mass spectrometric methods, allowing the identification of three internal sub-complexes with discrete functions in the kinetochore.
55. •] is used to dissect evolutionarily conserved interactions in the kinetochore.
56. C. Shang, T.R. Hazbun, I.M. Cheeseman, J. Aranda, S. Fields, D.G. Drubin, and G. Barnes Kinetochore protein interactions and their regulation by the Aurora kinase Ipl1p Mol Biol Cell 14 2003 3342 3355
57. P.A. Wigge, O.N. Jensen, S. Holmes, S. Soues, M. Mann, and J.V. Kilmartin Analysis of the Saccharomyces spindle pole by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry J Cell Biol 141 1998 967 977
58. J.S. Andersen, C.J. Wilkinson, T. Mayor, P. Mortensen, E.A. Nigg, and M. Mann Proteomic characterization of the human centrosome by protein correlation profiling Nature 426 2003 570 574 This detailed proteomic analysis of the centrosome reveals many dozens of new components.
59. A.J. Liska, A.V. Popov, S. Sunyaev, P. Coughlin, B. Habermann, A. Shevchenko, P. Bork, and E. Karsenti Homology-based functional proteomics by mass spectrometry: Application to the Xenopus microtubule-associated proteome Proteomics 4 2004 2707 2721
60. A.R. Skop, H. Liu, J. Yates III, B.J. Meyer, and R. Heald Dissection of the mammalian midbody proteome reveals conserved cytokinesis mechanisms Science 305 2004 61 66 Purified mammalian midbody preparations are subjected to multidimensional separation and mass spectrometric analysis (MudPIT). Of 160 candidate midbody components across a variety of functional categories, many were implicated in cytokinetic events by RNAi knockdown of the C. elegans orthologs.
61. A.C. Martin, and D.G. Drubin Impact of genome-wide functional analyses on cell biology research Curr Opin Cell Biol 15 2003 6 13
62. P. Jorgensen, J.L. Nishikawa, B.J. Breitkreutz, and M. Tyers Systematic identification of pathways that couple cell growth and division in yeast Science 297 2002 395 400 Direct cell size analysis of all ∼6,000 yeast deletion strains reveals hundreds of candidate size regulators, which are further classified by secondary genetic screens, microarray analysis and informatics.
63. J. Zhang, C. Schneider, L. Ottmers, R. Rodriguez, A. Day, J. Markwardt, and B.L. Schneider Genomic scale mutant hunt identifies cell size homeostasis genes in S. cerevisiae Curr Biol 12 2002 1992 2001
64. M.F. Zettel, L.R. Garza, A.M. Cass, R.A. Myhre, L.A. Haizlip, S.N. Osadebe, D.W. Sudimack, R. Pathak, T.L. Stone, and M. Polymenis The budding index of Saccharomyces cerevisiae deletion strains identifies genes important for cell cycle progression FEMS Microbiol Lett 223 2003 253 258
65. T.L. Saito, M. Ohtani, H. Sawai, F. Sano, A. Saka, D. Watanabe, M. Yukawa, Y. Ohya, and S. Morishita SCMD: Saccharomyces cerevisiae Morphological Database Nucleic Acids Res 32 Database issue 2004 D319 D322
66. •], the cell size regulator Whi5 is shown to bind the G1/S transcription factor SBF in a manner that is opposed by CDK activity.
67. •].
68. D. Huang, and D. Koshland Chromosome integrity in Saccharomyces cerevisiae: the interplay of DNA replication initiation factors, elongation factors, and origins Genes Dev 17 2003 1741 1754 A yeast artifical chromsome (YAC)-based assay identifies many gene deletion strains that have elevated GCR rates.
69. K.P. Rabitsch, A. Toth, M. Galova, A. Schleiffer, G. Schaffner, E. Aigner, C. Rupp, A.M. Penkner, A.C. Moreno-Borchart, and M. Primig A screen for genes required for meiosis and spore formation based on whole-genome expression Curr Biol 11 2001 1001 1009
70. •].
71. •].
72. •].
73. S. Mnaimneh, A.P. Davierwala, J. Haynes, J. Moffat, W.T. Peng, W. Zhang, X. Yang, J. Pootoolal, G. Chua, and A. Lopez Exploration of essential gene functions via titratable promoter alleles Cell 118 2004 31 44 A collection of ∼600 tet-regulated alleles of essential genes is used to reveal novel terminal phenotypes, including G1 arrest caused by the deletion of several ribosome biogenesis factors.
74. M. Kanemaki, A. Sanchez-Diaz, A. Gambus, and K. Labib Functional proteomic identification of DNA replication proteins by induced proteolysis in vivo Nature 423 2003 720 724 Temperature sensitive 'degron' conditional alleles are created for ∼60 uncharacterized essential genes, including three previously uncharacterized factors that form the GINS complex required for replication fork progression.
75. T. Matsumura, T. Yuasa, T. Hayashi, T. Obara, Y. Kimata, and M. Yanagida A brute force postgenome approach to identify temperature-sensitive mutations that negatively interact with separase and securin plasmids Genes Cells 8 2003 341 355
76. P. Gonczy, C. Echeverri, K. Oegema, A. Coulson, S.J. Jones, R.R. Copley, J. Duperon, J. Oegema, M. Brehm, and E. Cassin Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III Nature 408 2000 331 336
77. A. Desai, S. Rybina, T. Muller-Reichert, A. Shevchenko, A. Hyman, and K. Oegema KNL-1 directs assembly of the microtubule-binding interface of the kinetochore in C. elegans Genes Dev 17 2003 2421 2435
78. N. Le Bot, M.C. Tsai, R.K. Andrews, and J. Ahringer TAC-1, a regulator of microtubule length in the C. elegans embryo Curr Biol 13 2003 1499 1505
79. J. Pothof, G. van Haaften, K. Thijssen, R.S. Kamath, A.G. Fraser, J. Ahringer, R.H. Plasterk, and M. Tijsterman Identification of genes that protect the C. elegans genome against mutations by genome-wide RNAi Genes Dev 17 2003 443 448
80. S.S. Lee, R.Y. Lee, A.G. Fraser, R.S. Kamath, J. Ahringer, and G. Ruvkun A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity Nat Genet 33 2003 40 48
81. A. Kiger, B. Baum, S. Jones, M. Jones, A. Coulson, C. Echeverri, and N. Perrimon A functional genomic analysis of cell morphology using RNA interference J Biol 2 2003 27
82. M. Boutros, A.A. Kiger, S. Armknecht, K. Kerr, M. Hild, B. Koch, S.A. Haas, H.F. Consortium, R. Paro, and N. Perrimon Genome-wide RNAi analysis of growth and viability in Drosophila cells Science 303 2004 832 835 A high-throughput RNAi-based screen of 19470 double-stranded RNAs in tissue culture cells reveals at least 438 genes required for viability, including known cell-cycle-regulatory genes.
83. P.J. Paddison, J.M. Silva, D.S. Conklin, M. Schlabach, M. Li, S. Aruleba, V. Balija, A. O'Shaughnessy, L. Gnoj, and K. Scobie A resource for large-scale RNA-interference-based screens in mammals Nature 428 2004 427 431 Construction of a barcoded shRNA expression library that targets nearly 10000 human genes and >5000 mouse genes.
84. K. Berns, E.M. Hijmans, J. Mullenders, T.R. Brummelkamp, A. Velds, M. Heimerikx, R.M. Kerkhoven, M. Madiredjo, W. Nijkamp, and B. Weigelt A large-scale RNAi screen in human cells identifies new components of the p53 pathway Nature 428 2004 431 437 Construction of an shRNA library that targets nearly 8000 human genes. A new modulator of p53 is identified in a pilot screen.
85. J.C. Neil, and E.R. Cameron Retroviral insertion sites and cancer: fountain of all knowledge? Cancer Cell 2 2002 253 255
86. Kip1 loss by insertional mutagenesis and high-throughput insertion site analysis Proc Natl Acad Sci USA 99 2002 11293 11298
87. D. Huang, J. Moffat, and B. Andrews Dissection of a complex phenotype by functional genomics reveals roles for the yeast cyclin-dependent protein kinase Pho85 in stress adaptation and cell integrity Mol Cell Biol 22 2002 5076 5088 An SGA screen, combined with other functional genomics tests, uncovers multiple functions of the Pho85 cyclin-dependent kinase.
88. H. Xu, C. Boone, and H.L. Klein Mrc1 is required for sister chromatid cohesion to aid in recombination repair of spontaneous damage Mol Cell Biol 24 2004 7082 7090
89. M.L. Mayer, I. Pot, M. Chang, H. Xu, V. Aneliunas, T. Kwok, R. Newitt, R. Aebersold, C. Boone, and G.W. Brown Identification of protein complexes required for efficient sister chromatid cohesion Mol Biol Cell 15 2004 1736 1745 An SGA screen with a strain lacking the cohesion factor Ctf8 uncovers new gene functions required for cohesion, including an unanticipated role for mitotic spindle components.
90. B. Nelson, C. Kurischko, J. Horecka, M. Mody, P. Nair, L. Pratt, A. Zougman, L.D. McBroom, T.R. Hughes, and C. Boone RAM: a conserved signaling network that regulates Ace2p transcriptional activity and polarized morphogenesis Mol Biol Cell 14 2003 3782 3803 The RAM signaling network that governs the daughter-cell-specific transcription factor Ace2 is elaborated by SGA screens, two-hybrid interactions and co-precipitation interactions.
91. A.S. Goehring, D.A. Mitchell, A.H. Tong, M.E. Keniry, C. Boone, and G.F. Sprague Jr. Synthetic lethal analysis implicates Ste20p, a p21-activated protein kinase, in polarisome activation Mol Biol Cell 14 2003 1501 1516
92. K.K. Baetz, N.J. Krogan, A. Emili, J. Greenblatt, and P. Hieter The ctf13-30/CTF13 genomic haploinsufficiency modifier screen identifies the yeast chromatin remodeling complex RSC, which is required for the establishment of sister chromatid cohesion Mol Cell Biol 24 2004 1232 1244
93. P. Jorgensen, B. Nelson, M.D. Robinson, Y. Chen, B. Andrews, M. Tyers, and C. Boone High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutants Genetics 162 2002 1091 1099
94. Jorgensen P, Rupes I, Sharom JR, Schneper L, Broach JR, Tyers M: A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev 2004, in press. Regulation of the RP and Ribi regulons correlates with the dynamic localization of Sfp1, the Akt-like kinase Sch9, and two RP-specific transcription factors, Fhl1 and Ifh1.
95. Marion RM, Regev A, Segal E, Barash Y, Koller D, Friedman N, O'Shea EK: Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression. Proc Natl Acad Sci U S A 2004, in press. Systematic localization studies (see [9]) lead to the discovery that Sfp1 localization responds rapidly to nutirent source shifts with concomitant changes in RP and Ribi gene expression.
96. J. Grigull, S. Mnaimneh, J. Pootoolal, M.D. Robinson, and T.R. Hughes Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors Mol Cell Biol 24 2004 5534 5547
97. Dez C, Tollervey D: Yeast ribosome biogenesis meets the cell cycle. Curr Opin Microbiol 2004, in press.
98. R.N. Eisenman Deconstructing Myc Genes Dev 15 2001 2023 2030
99. A. Orian, B. van Steensel, J. Delrow, H.J. Bussemaker, L. Li, T. Sawado, E. Williams, L.W. Loo, S.M. Cowley, and C. Yost Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network Genes Dev 17 2003 1101 1114 Genome-wide determination of Myc network interactions on promoter DNA by the DamID method reveals that Myc binds to ∼15% of all coding regions, including many ribosome biogenesis genes.
100. D. Ruggero, and P.P. Pandolfi Does the ribosome translate cancer? Nat Rev Cancer 3 2003 179 192
101. H.F. Horn, and K.H. Vousden Cancer: guarding the guardian? Nature 427 2004 110 111
102. A. Amsterdam, K.C. Sadler, K. Lai, S. Farrington, R.T. Bronson, J.A. Lees, and N. Hopkins Many ribosomal protein genes are cancer genes in zebrafish PLoS Biol 2 2004 E139
103. H.M. Sauro, M. Hucka, A. Finney, C. Wellock, H. Bolouri, J. Doyle, and H. Kitano Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration Omics 7 2003 355 372
104. F.R. Cross, V. Archambault, M. Miller, and M. Klovstad Testing a mathematical model of the yeast cell cycle Mol Biol Cell 13 2002 52 70 One of the first comprehensive efforts to combine modeling with quantitative analysis of critical regulators and experimental tests.
105. K.C. Chen, L. Calzone, A. Csikasz-Nagy, F.R. Cross, B. Novak, and J.J. Tyson Integrative analysis of cell cycle control in budding yeast Mol Biol Cell 15 2004 3841 3862 The latest inception of a systematic mathematical model of the yeast cell cycle.
106. D. Angeli, J.E. Ferrell Jr., and E.D. Sontag Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems Proc Natl Acad Sci USA 101 2004 1822 1827
107. F. Li, T. Long, Y. Lu, Q. Ouyang, and C. Tang The yeast cell-cycle network is robustly designed Proc Natl Acad Sci USA 101 2004 4781 4786 The essential features of the yeast cell cycle are modeled in an 11-node network, which is then analyzed for its behavior as a dynamic attractor.
108. E.H. Davidson, J.P. Rast, P. Oliveri, A. Ransick, C. Calestani, C.H. Yuh, T. Minokawa, G. Amore, V. Hinman, and C. Arenas-Mena A genomic regulatory network for development Science 295 2002 1669 1678
109. T. Pramila, S. Miles, D. GuhaThakurta, D. Jemiolo, and L.L. Breeden Conserved homeodomain proteins interact with MADS box protein Mcm1 to restrict ECB-dependent transcription to the M/G1 phase of the cell cycle Genes Dev 16 2002 3034 3045
110. A. Echard, G.R.X. Hickson, E. Foley, and P.H. O'Farrell Terminal cytokinesis events uncovered after RNAi screen Curr Biol 14 2004 1685 1693 A visual screen for multinucleate cells resulting from aberrant cytokinesis is carried out with over 7000 dsRNAs that represent conserved Drosophila genes. Of 30 dsRNAs that cause multinucleate cells, 17 correspond to genes not previously implicated in cytokinesis, 11 of which are entirely novel.
111. E. Hernando, Z. Nahle, G. Juan, E. Diaz-Rodriguez, M. Alaminos, M. Hemann, L. Michel, V. Mittal, W. Gerald, and R. Benezra Rb inactivation promotes genomic instability by uncoupling cell cycle progression from mitotic control Nature 430 2004 797 802 Prompted by global gene expression profiles and chromatin immunoprecipitation experiments that indicated MAD2 is an E2F target, the authors go on to discover an unanticipated direct link between Rb inactivation and chromosome instability, which may help account for frequent aneuploidy in human cancer.