Commitment to a Cellular Transition Precedes Genome-wide Transcriptional Change
Tài liệu tham khảo
Amon, 1993, Mechanisms that help the yeast cell cycle clock tick: G2 cyclins transcriptionally activate G2 cyclins and repress G1 cyclins, Cell, 74, 993, 10.1016/0092-8674(93)90722-3
Andrews, 1989, Identification of a DNA binding factor involved in cell-cycle control of the yeast HO gene, Cell, 57, 21, 10.1016/0092-8674(89)90168-2
Bai, 2010, Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle, Dev. Cell, 18, 544, 10.1016/j.devcel.2010.02.007
Bean, 2006, Coherence and timing of cell cycle start examined at single-cell resolution, Mol. Cell, 21, 3, 10.1016/j.molcel.2005.10.035
Blagosklonny, 2002, The restriction point of the cell cycle, Cell Cycle, 1, 103, 10.4161/cc.1.2.108
Borun, 1975, Further evidence of transcriptional and translational control of histone messenger RNA during the HeLa S3 cycle, Cell, 4, 59, 10.1016/0092-8674(75)90134-8
Bracken, 2004, E2F target genes: unraveling the biology, Trends Biochem. Sci., 29, 409, 10.1016/j.tibs.2004.06.006
Brauer, 2008, Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast, Mol. Biol. Cell, 19, 352, 10.1091/mbc.e07-08-0779
Chechik, 2009, Timing of gene expression responses to environmental changes, J. Comput. Biol., 16, 279, 10.1089/cmb.2008.13TT
Chechik, 2008, Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network, Nat. Biotechnol., 26, 1251, 10.1038/nbt.1499
Cho, 1998, A genome-wide transcriptional analysis of the mitotic cell cycle, Mol. Cell, 2, 65, 10.1016/S1097-2765(00)80114-8
Cliften, 2003, Finding functional features in Saccharomyces genomes by phylogenetic footprinting, Science, 301, 71, 10.1126/science.1084337
Costanzo, 2004, CDK activity antagonizes Whi5, an inhibitor of G1/S transcription in yeast, Cell, 117, 899, 10.1016/j.cell.2004.05.024
Darieva, 2010, A competitive transcription factor binding mechanism determines the timing of late cell cycle-dependent gene expression, Mol. Cell, 38, 29, 10.1016/j.molcel.2010.02.030
de Bruin, 2004, Cln3 activates G1-specific transcription via phosphorylation of the SBF bound repressor Whi5, Cell, 117, 887, 10.1016/j.cell.2004.05.025
de Bruin, 2006, Constraining G1-specific transcription to late G1 phase: the MBF-associated corepressor Nrm1 acts via negative feedback, Mol. Cell, 23, 483, 10.1016/j.molcel.2006.06.025
Di Talia, 2009, Daughter-specific transcription factors regulate cell size control in budding yeast, PLoS Biol., 7, e1000221, 10.1371/journal.pbio.1000221
Dirick, 1995, Roles and regulation of Cln-Cdc28 kinases at the start of the cell cycle of Saccharomyces cerevisiae, EMBO J., 14, 4803, 10.1002/j.1460-2075.1995.tb00162.x
Dončić, 2011, Distinct interactions select and maintain a specific cell fate, Mol. Cell, 43, 528, 10.1016/j.molcel.2011.06.025
Elledge, 1990, Two genes differentially regulated in the cell cycle and by DNA-damaging agents encode alternative regulatory subunits of ribonucleotide reductase, Genes Dev., 4, 740, 10.1101/gad.4.5.740
Ferrezuelo, 2010, The transcriptional network activated by Cln3 cyclin at the G1-to-S transition of the yeast cell cycle, Genome Biol., 11, R67, 10.1186/gb-2010-11-6-r67
Flick, 1998, Regulation of cell size by glucose is exerted via repression of the CLN1 promoter, Mol. Cell. Biol., 18, 2492, 10.1128/MCB.18.5.2492
Georgi, 2002, Timing of events in mitosis, Curr. Biol., 12, 105, 10.1016/S0960-9822(01)00662-5
Ghaemmaghami, 2003, Global analysis of protein expression in yeast, Nature, 425, 737, 10.1038/nature02046
Guan, 2010, Systematic planning of genome-scale experiments in poorly studied species, PLoS Comput. Biol., 6, e1000698, 10.1371/journal.pcbi.1000698
Hartwell, 1989, Checkpoints: controls that ensure the order of cell cycle events, Science, 246, 629, 10.1126/science.2683079
Hartwell, 1974, Genetic control of the cell division cycle in yeast, Science, 183, 46, 10.1126/science.183.4120.46
Hereford, 1981, Cell-cycle regulation of yeast histone mRNA, Cell, 24, 367, 10.1016/0092-8674(81)90326-3
Holt, 2008, Positive feedback sharpens the anaphase switch, Nature, 454, 353, 10.1038/nature07050
Jensen, 2006, Co-evolution of transcriptional and post-translational cell-cycle regulation, Nature, 443, 594, 10.1038/nature05186
Johnson, 1994, Autoregulatory control of E2F1 expression in response to positive and negative regulators of cell cycle progression, Genes Dev., 8, 1514, 10.1101/gad.8.13.1514
Justman, 2009, Tuning the activation threshold of a kinase network by nested feedback loops, Science, 324, 509, 10.1126/science.1169498
Kalir, 2001, Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria, Science, 292, 2080, 10.1126/science.1058758
Kato, 2004, Identifying combinatorial regulation of transcription factors and binding motifs, Genome Biol., 5, R56, 10.1186/gb-2004-5-8-r56
Koch, 1993, A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase, Science, 261, 1551, 10.1126/science.8372350
Lam, 2008, Chromatin decouples promoter threshold from dynamic range, Nature, 453, 246, 10.1038/nature06867
Laub, 2000, Global analysis of the genetic network controlling a bacterial cell cycle, Science, 290, 2144, 10.1126/science.290.5499.2144
Levy, 2007, Strategy of transcription regulation in the budding yeast, PLoS ONE, 2, e250, 10.1371/journal.pone.0000250
López-Avilés, 2009, Irreversibility of mitotic exit is the consequence of systems-level feedback, Nature, 459, 592, 10.1038/nature07984
MacKay, 2001, Early cell cycle box-mediated transcription of CLN3 and SWI4 contributes to the proper timing of the G(1)-to-S transition in budding yeast, Mol. Cell. Biol., 21, 4140, 10.1128/MCB.21.13.4140-4148.2001
Markey, 2002, Unbiased analysis of RB-mediated transcriptional repression identifies novel targets and distinctions from E2F action, Cancer Res., 62, 6587
Mateus, 2000, Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry, Yeast, 16, 1313, 10.1002/1097-0061(200010)16:14<1313::AID-YEA626>3.0.CO;2-O
Mogno, 2010, TATA is a modular component of synthetic promoters, Genome Res., 20, 1391, 10.1101/gr.106732.110
Morgan, 2007
Müller, 2001, E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis, Genes Dev., 15, 267, 10.1101/gad.864201
Nasmyth, 1991, The role of SWI4 and SWI6 in the activity of G1 cyclins in yeast, Cell, 66, 995, 10.1016/0092-8674(91)90444-4
Oliva, 2005, The cell cycle-regulated genes of Schizosaccharomyces pombe, PLoS Biol., 3, e225, 10.1371/journal.pbio.0030225
Orlando, 2008, Global control of cell-cycle transcription by coupled CDK and network oscillators, Nature, 453, 944, 10.1038/nature06955
Peng, 2005, Identification of cell cycle-regulated genes in fission yeast, Mol. Biol. Cell, 16, 1026, 10.1091/mbc.e04-04-0299
Planas-Silva, 1997, The restriction point and control of cell proliferation, Curr. Opin. Cell Biol., 9, 768, 10.1016/S0955-0674(97)80076-2
Pomerening, 2003, Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2, Nat. Cell Biol., 5, 346, 10.1038/ncb954
Pramila, 2006, The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle, Genes Dev., 20, 2266, 10.1101/gad.1450606
Ren, 2002, E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints, Genes Dev., 16, 245, 10.1101/gad.949802
Rustici, 2004, Periodic gene expression program of the fission yeast cell cycle, Nat. Genet., 36, 809, 10.1038/ng1377
Shen-Orr, 2002, Network motifs in the transcriptional regulation network of Escherichia coli, Nat. Genet., 31, 64, 10.1038/ng881
Skotheim, 2008, Positive feedback of G1 cyclins ensures coherent cell cycle entry, Nature, 454, 291, 10.1038/nature07118
Spellman, 1998, Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization, Mol. Biol. Cell, 9, 3273, 10.1091/mbc.9.12.3273
Stuart, 1995, CLN3, not positive feedback, determines the timing of CLN2 transcription in cycling cells, Genes Dev., 9, 2780, 10.1101/gad.9.22.2780
Tirosh, 2006, A genetic signature of interspecies variations in gene expression, Nat. Genet., 38, 830, 10.1038/ng1819
Tyers, 1993, Comparison of the Saccharomyces cerevisiae G1 cyclins: Cln3 may be an upstream activator of Cln1, Cln2 and other cyclins, EMBO J., 12, 1955, 10.1002/j.1460-2075.1993.tb05845.x
Whitfield, 2002, Identification of genes periodically expressed in the human cell cycle and their expression in tumors, Mol. Biol. Cell, 13, 1977, 10.1091/mbc.02-02-0030
Wijnen, 2002, The G(1) cyclin Cln3 promotes cell cycle entry via the transcription factor Swi6, Mol. Cell. Biol., 22, 4402, 10.1128/MCB.22.12.4402-4418.2002
Xiong, 2003, A positive-feedback-based bistable ‘memory module’ that governs a cell fate decision, Nature, 426, 460, 10.1038/nature02089
Xu, 2007, A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members, Genome Res., 17, 1550, 10.1101/gr.6783507
Yao, 2008, A bistable Rb-E2F switch underlies the restriction point, Nat. Cell Biol., 10, 476, 10.1038/ncb1711
Yung, 2007, A Skp2 autoinduction loop and restriction point control, J. Cell Biol., 178, 741, 10.1083/jcb.200703034
Zaslaver, 2004, Just-in-time transcription program in metabolic pathways, Nat. Genet., 36, 486, 10.1038/ng1348