Recipes and mechanisms of cellular reprogramming: A case study on budding yeast Saccharomyces cerevisiae

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Ding, Shengchao ^a   Wang, Wei ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

ARTICLE; BIOLOGICAL MODEL; CELL CYCLE; CELL TRANSDIFFERENTIATION; FUNGUS SPORE; GENE REGULATORY NETWORK; GROWTH, DEVELOPMENT AND AGING; MUTATION; PHENOTYPE; PHYSIOLOGY; PLURIPOTENT STEM CELL; SACCHAROMYCES CEREVISIAE;

CELL CYCLE; CELL TRANSDIFFERENTIATION; GENE REGULATORY NETWORKS; INDUCED PLURIPOTENT STEM CELLS; MODELS, GENETIC; MUTATION; PHENOTYPE; SACCHAROMYCES CEREVISIAE; SPORES, FUNGAL;

EID: 79953900886     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-50     Document Type: Article

References (46)

1. Waddington CH. The strategy of the genes. 1957, London: Allen & Unwin.
2. Graf T, Enver T. Forcing cells to change lineages. Nature 2009, 462:587-594. 10.1038/nature08533, 19956253.
3. Huang S, Eichler G, Bar-Yam Y, Ingber DE. Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys Rev Lett 2005, 94:128701. 10.1103/PhysRevLett.94.128701, 15903968.
4. Huang S. Cell lineage determination in state space: a systems view brings flexibility to dogmatic canonical rules. PLoS Biol 2010, 8:e1000380. 10.1371/journal.pbio.1000380, 2876052, 20520792.
5. Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006, 126:663-676. 10.1016/j.cell.2006.07.024, 16904174.
6. Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R, et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 2007, 318:1917-1920. 10.1126/science.1151526, 18029452.
7. Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 2007, 131:861-872. 10.1016/j.cell.2007.11.019, 18035408.
8. Saha K, Jaenisch R. Technical challenges in using human induced pluripotent stem cells to model disease. Cell Stem Cell 2009, 5:584-595. 10.1016/j.stem.2009.11.009, 2921621, 19951687.
9. McGary K, Lee I, Marcotte E. Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biology 2007, 8:R258. 10.1186/gb-2007-8-12-r258, 2246260, 18053250.
10. Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet 2008, 40:181-188. 10.1038/ng.2007.70, 18223650.
11. Han B, Wang J. Quantifying Robustness and Dissipation Cost of Yeast Cell Cycle Network: The Funneled Energy Landscape Perspectives. Biophysical Journal 2007, 92:3755-3763. 10.1529/biophysj.106.094821, 1868985, 17350995.
12. Wang J, Xu L, Wang E, Huang S. The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation. Biophys J 2010, 99:29-39. 10.1016/j.bpj.2010.03.058, 20655830.
13. Kauffman S. Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology 1969, 22:437-467. 10.1016/0022-5193(69)90015-0, 5803332.
14. D'Amours D, Amon A. At the interface between signaling and executing anaphase--Cdc14 and the FEAR network. Genes & Development 2004, 18:2581-2595.
15. Kassir Y, Adir N, Boger-Nadjar E, Raviv NG, Rubin-Bejerano I, Sagee S, Shenhar G. Transcriptional regulation of meiosis in budding yeast. International review of cytology 2003, 224:111-171. full_text, 12722950.
16. Li F, Long T, Lu Y, Ouyang Q, Tang C. The yeast cell-cycle network is robustly designed. PNAS 2004, 101:4781-4786. 10.1073/pnas.0305937101, 387325, 15037758.
17. Tyers M, Tokiwa G, Futcher B. Comparison of the Saccharomyces cerevisiae G1 cyclins: Cln3 may be an upstream activator of Cln1, Cln2 and other cyclins. EMBO J 1993, 12:1955. 413417, 8387915.
18. Costanzo M, Nishikawa JL, Tang X, Millman JS, Schub O, Breitkreuz K, Dewar D, Rupes I, Andrews B, Tyers M. CDK Activity Antagonizes Whi5, an Inhibitor of G1/S Transcription in Yeast. Cell 2004, 117:899-913. 10.1016/j.cell.2004.05.024, 15210111.
19. Schwob E, Nasmyth K. CLB5 and CLB6, a new pair of B cyclins involved in DNA replication in Saccharomyces cerevisiae. Genes & Development 1993, 7:1160-1175.
20. Schwob E, Böhm T, Mendenhall MD, Nasmyth K. The B-type cyclin kinase inhibitor p40SIC1 controls the G1 to S transition in S. cerevisiae. Cell 1994, 79:233-244. 10.1016/0092-8674(94)90193-7, 7954792.
21. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization. Mol Biol Cell 1998, 9:3273-3297. 25624, 9843569.
22. Friedlander G, Joseph-Strauss D, Carmi M, Zenvirth D, Simchen G, Barkai N. Modulation of the transcription regulatory program in yeast cells committed to sporulation. Genome Biol 2006, 7:R20. 10.1186/gb-2006-7-3-r20, 1557749, 16542486.
23. Barral Y, Jentsch S, Mann C. G1 cyclin turnover and nutrient uptake are controlled by a common pathway in yeast. Genes & Development 1995, 9:399-409.
24. Li FN, Johnston M. Grr1 of Saccharomyces cerevisiae is connected to the ubiquitin proteolysis machinery through Skp1: coupling glucose sensing to gene expression and the cell cycle. EMBO J 1997, 16:5629-5638. 10.1093/emboj/16.18.5629, 1170195, 9312022.
25. Prinz S, Hwang ES, Visintin R, Amon A. The regulation of Cdc20 proteolysis reveals a role for the APC components Cdc23 and Cdc27 during S phase and early mitosis. Current Biology 1998, 8:750-760. 10.1016/S0960-9822(98)70298-2, 9651679.
26. Zachariae W, Schwab M, Nasmyth K, Seufert W. Control of Cyclin Ubiquitination by CDK-Regulated Binding of Hct1 to the Anaphase Promoting Complex. Science 1998, 282:1721-1724. 10.1126/science.282.5394.1721, 9831566.
27. Yanagida M. Cell cycle mechanisms of sister chromatid separation; roles of Cut1/separin and Cut2/securin. Genes to Cells 2000, 5:1-8. 10.1046/j.1365-2443.2000.00306.x, 10651900.
28. Nasmyth K, Peters JM, Uhlmann F. Splitting the Chromosome: Cutting the Ties That Bind Sister Chromatids. Science 2000, 288:1379-1384. 10.1126/science.288.5470.1379, 10827941.
29. Cooper KF, Mallory MJ, Guacci V, Lowe K, Strich R. Pds1p Is Required for Meiotic Recombination and Prophase I Progression in Saccharomyces cerevisiae. Genetics 2009, 181:65-79. 10.1534/genetics.108.095513, 2621190, 19001291.
30. Cohen-Fix O, Peters JM, Kirschner MW, Koshland D. Anaphase initiation in Saccharomyces cerevisiae is controlled by the APC-dependent degradation of the anaphase inhibitor Pds1p. Genes & Development 1996, 10:3081-3093.
31. Cohen-Fix O, Koshland D. The anaphase inhibitor of Saccharomyces cerevisiae Pds1p is a target of the DNA damage checkpoint pathway. Proceedings of the National Academy of Sciences of the United States of America 1997, 94:14361-14366. 10.1073/pnas.94.26.14361, 24978, 9405617.
32. Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, Tyson JJ. Integrative Analysis of Cell Cycle Control in Budding Yeast. Mol Biol Cell 2004, 15:3841-3862. 10.1091/mbc.E03-11-0794, 491841, 15169868.
33. Deutschbauer AM, Williams RM, Chu AM, Davis RW. Parallel phenotypic analysis of sporulation and postgermination growth in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America 2002, 99:15530-15535. 10.1073/pnas.202604399, 137751, 12432101.
34. Dwight S, Harris M, Dolinski K, Ball C, Binkley G, Christie K, Fisk D, Issel-Tarver L, Schroeder M, Sherlock G. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res 2002, 30:69-72. 10.1093/nar/30.1.69, 99086, 11752257.
35. Vidal M, Gaber RF. RPD3 encodes a second factor required to achieve maximum positive and negative transcriptional states in Saccharomyces cerevisiae. Mol Cell Biol 1991, 11:6317-6327. 361826, 1944291.
36. Schüller HJ. Transcriptional control of nonfermentative metabolism in the yeast Saccharomyces cerevisiae. Current Genetics 2003, 43:139-160.
37. Wang W, Cherry JM, Nochomovitz Y, Jolly E, Botstein D, Li H. Inference of combinatorial regulation in yeast transcriptional networks: A case study of sporulation. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:1998-2003. 10.1073/pnas.0405537102, 548531, 15684073.
38. Graf T, Stadtfeld M. Heterogeneity of embryonic and adult stem cells. Cell Stem Cell 2008, 3:480-483. 10.1016/j.stem.2008.10.007, 18983963.
39. Godfrey P, Shipley R, Gryz J. Algorithms and analyses for maximal vector computation. The VLDB Journal 2007, 16:5-28.
40. Lutfiyya LL, Iyer VR, DeRisi J, DeVit MJ, Brown PO, Johnston M. Characterization of Three Related Glucose Repressors and Genes They Regulate in Saccharomyces cerevisiae. Genetics 1998, 150:1377-1391. 1460414, 9832517.
41. Ma W, Trusina A, El-Samad H, Lim WA, Tang C. Defining network topologies that can achieve biochemical adaptation. Cell 2009, 138:760-773. 10.1016/j.cell.2009.06.013, 3068210, 19703401.
42. Yamanaka S. Elite and stochastic models for induced pluripotent stem cell generation. Nature 2009, 460:49-52. 10.1038/nature08180, 19571877.
43. Irons DJ. Logical analysis of the budding yeast cell cycle. Journal of Theoretical Biology 2009, 257:543-559. 10.1016/j.jtbi.2008.12.028, 19185585.
44. Shen L, Chepelev I, Liu J, Wang W. Prediction of quantitative phenotypes based on genetic networks: a case study in yeast sporulation. BMC Systems Biology 2010, 4:128. 10.1186/1752-0509-4-128, 2944141, 20828418.
45. Visintin R, Craig K, Hwang E, Prinz S, Tyers M, Amon A. The phosphatase Cdc14 triggers mitotic exit by reversal of Cdk-dependent phosphorylation. Mol Cell 1998, 2:709-718. 10.1016/S1097-2765(00)80286-5, 9885559.
46. Baldi P, Brunak S, Chauvin Y, Andersen CAF, Nielsen H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 2000, 16:412-424. 10.1093/bioinformatics/16.5.412, 10871264.