Comprehensive Analysis of Combinatorial Regulation using the Transcriptional Regulatory Network of Yeast

Journal of Molecular Biology

Volumn 360, Issue 1, 2006, Pages 213-227

  Balaji, S ^a   Babu, M Madan ^a   Iyer, Lakshminarayan M ^a   Luscombe, Nicholas M ^b   Aravind, L ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

co regulation network; evolution; signal transduction; transcriptional network; ubiquitin pathway

Indexed keywords

TRANSCRIPTION FACTOR; UBIQUITIN PROTEIN LIGASE; UBIQUITIN PROTEIN LIGASE E3;

ARTICLE; EUKARYOTE; FUNGAL STRAIN; GENE CONTROL; GENE EXPRESSION; GENE TARGETING; GENOME; GENOME ANALYSIS; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; STATISTICAL SIGNIFICANCE; TRANSCRIPTION REGULATION; YEAST;

EUKARYOTA;

EID: 33745449162     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.04.029     Document Type: Article

References (59)

1. Ptashne M. Regulation of transcription: from lambda to eukaryotes. Trends Biochem. Sci. 30 (2005) 275-279
2. Ptashne M. Genetic Switch: Phage Lambda Revisited. 3rd edit. (2004), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
3. Ptashne M., and Gann A. Genes and Signals. 1st edit. (2001), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
4. Levine M., and Tjian R. Transcription regulation and animal diversity. Nature 424 (2003) 147-151
5. Davidson E.H. Genomic Regulatory Systems: Development and Evolution. 1st edit. (2001), Academic Press, San Deigo, CA
6. Inoue T., Wang M., Ririe T.O., Fernandes J.S., and Sternberg P.W. Transcriptional network underlying Caenorhabditis elegans vulval development. Proc. Natl Acad. Sci. USA 102 (2005) 4972-4977
7. Revilla-i-Domingo R., and Davidson E.H. Developmental gene network analysis. Int. J. Dev. Biol. 47 (2003) 695-703
8. Davidson E.H., Rast J.P., Oliveri P., Ransick A., Calestani C., Yuh C.H., et al. A genomic regulatory network for development. Science 295 (2002) 1669-1678
9. Wathelet M.G., Lin C.H., Parekh B.S., Ronco L.V., Howley P.M., and Maniatis T. Virus infection induces the assembly of coordinately activated transcription factors on the IFN-beta enhancer in vivo. Mol. Cell 1 (1998) 507-518
10. Chen L., Glover J.N., Hogan P.G., Rao A., and Harrison S.C. Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA. Nature 392 (1998) 42-48
11. Thanos D., and Maniatis T. Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell 83 (1995) 1091-1100
12. Britten R.J., and Davidson E.H. Gene regulation for higher cells: a theory. Science 165 (1969) 349-357
13. Newman J.R., and Keating A.E. Comprehensive identification of human bZIP interactions with coiled-coil arrays. Science 300 (2003) 2097-2101
14. Tan S., and Richmond T.J. Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex. Nature 391 (1998) 660-666
15. Mannervik M., Nibu Y., Zhang H., and Levine M. Transcriptional coregulators in development. Science 284 (1999) 606-609
16. Klinkenberg L.G., Mennella T.A., Luetkenhaus K., and Zitomer R.S. Combinatorial repression of the hypoxic genes of Saccharomyces cerevisiae by DNA binding proteins Rox1 and Mot3. Eukaryot. Cell 4 (2005) 649-660
17. Mennella T.A., Klinkenberg L.G., and Zitomer R.S. Recruitment of Tup1-Ssn6 by yeast hypoxic genes and chromatin-independent exclusion of TATA binding protein. Eukaryot. Cell 2 (2003) 1288-1303
18. Sertil O., Kapoor R., Cohen B.D., Abramova N., and Lowry C.V. Synergistic repression of anaerobic genes by Mot3 and Rox1 in Saccharomyces cerevisiae. Nucl. Acids Res. 31 (2003) 5831-5837
19. Tsai H.K., Lu H.H., and Li W.H. Statistical methods for identifying yeast cell cycle transcription factors. Proc. Natl Acad. Sci. USA 102 (2005) 13532-13537
20. Nagamine N., Kawada Y., and Sakakibara Y. Identifying cooperative transcriptional regulations using protein-protein interactions. Nucl. Acids Res. 33 (2005) 4828-4837
21. Wang W., Cherry J.M., Nochomovitz Y., Jolly E., Botstein D., and Li H. Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proc. Natl Acad. Sci. USA 102 (2005) 1998-2003
22. Bluthgen N., Kielbasa S.M., and Herzel H. Inferring combinatorial regulation of transcription in silico. Nucl. Acids Res. 33 (2005) 272-279
23. Kato M., Hata N., Banerjee N., Futcher B., and Zhang M.Q. Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol. 5 (2004) R56
24. Pilpel Y., Sudarsanam P., and Church G.M. Identifying regulatory networks by combinatorial analysis of promoter elements. Nature Genet. 29 (2001) 153-159
25. GuhaThakurta D., and Stormo G.D. Identifying target sites for cooperatively binding factors. Bioinformatics 17 (2001) 608-621
26. Banerjee N., and Zhang M.Q. Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucl. Acids Res. 31 (2003) 7024-7031
27. Wagner A. Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics 15 (1999) 776-784
28. Babu M.M., Luscombe N.M., Aravind L., Gerstein M., and Teichmann S.A. Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol. 14 (2004) 283-291
29. Luscombe N.M., Babu M.M., Yu H., Snyder M., Teichmann S.A., and Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431 (2004) 308-312
30. Harbison C.T., Gordon D.B., Lee T.I., Rinaldi N.J., Macisaac K.D., Danford T.W., et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431 (2004) 99-104
31. Teichmann S.A., and Babu M.M. Gene regulatory network growth by duplication. Nature Genet. 36 (2004) 492-496
32. Horak C.E., Luscombe N.M., Qian J., Bertone P., Piccirrillo S., Gerstein M., and Snyder M. Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev. 16 (2002) 3017-3033
33. Lee T.I., Rinaldi N.J., Robert F., Odom D.T., Bar-Joseph Z., Gerber G.K., et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298 (2002) 799-804
34. Svetlov V.V., and Cooper T.G. Review: compilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae. Yeast 11 (1995) 1439-1484
35. Guelzim N., Bottani S., Bourgine P., and Kepes F. Topological and causal structure of the yeast transcriptional regulatory network. Nature Genet. 31 (2002) 60-63
36. Maslov S., and Sneppen K. Computational architecture of the yeast regulatory network. Phys. Biol. 2 (2005) S94-S100
37. Zaman Z., Heid C., and Ptashne M. Telomere looping permits repression "at a distance" in yeast. Curr. Biol. 12 (2002) 930-933
38. Martin D.E., Soulard A., and Hall M.N. TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1. Cell 119 (2004) 969-979
39. Andrews B.J., and Moore L.A. Interaction of the yeast Swi4 and Swi6 cell cycle regulatory proteins in vitro. Proc. Natl Acad. Sci. USA 89 (1992) 11852-11856
40. Nasmyth K., and Dirick L. The role of SWI4 and SWI6 in the activity of G1 cyclins in yeast. Cell 66 (1991) 995-1013
41. Ronen M., and Botstein D. Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source. Proc. Natl Acad. Sci. USA 103 2 (2005) 389-394
42. Petti A.A., and Church G.M. A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae. Genome Res. 15 (2005) 1298-1306
43. Milo R., Shen-Orr S., Itzkovitz S., Kashtan N., Chklovskii D., and Alon U. Network motifs: simple building blocks of complex networks. Science 298 (2002) 824-827
44. Ciechanover A. Intracellular protein degradation: from a vague idea, through the lysosome and the ubiquitin-proteasome system, and onto human diseases and drug targeting (Nobel lecture). Angew Chem. Int. Ed. Engl. 44 (2005) 5944-5967
45. Ciechanover A. Proteolysis: from the lysosome to ubiquitin and the proteasome. Nature Rev. Mol. Cell Biol. 6 (2005) 79-87
46. Finley D., Ciechanover A., and Varshavsky A. Ubiquitin as a central cellular regulator. Cell 116 (2004) S29-S32
47. Lespinet O., Wolf Y.I., Koonin E.V., and Aravind L. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 12 (2002) 1048-1059
48. Chervitz S.A., Aravind L., Sherlock G., Ball C.A., Koonin E.V., Dwight S.S., et al. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science 282 (1998) 2022-2028
49. Iyer L.M., Koonin E.V., and Aravind L. Novel predicted peptidases with a potential role in the ubiquitin signaling pathway. Cell Cycle 3 (2004) 1440-1450
50. Schaffer A.A., Wolf Y.I., Ponting C.P., Koonin E.V., Aravind L., and Altschul S.F. IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics 15 (1999) 1000-1011
51. London M.K., Keck B.I., Ramos P.C., and Dohmen R.J. Regulatory mechanisms controlling biogenesis of ubiquitin and the proteasome. FEBS Letters 567 (2004) 259-264
52. Xie Y., and Varshavsky A. RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: a negative feedback circuit. Proc. Natl Acad. Sci. USA 98 (2001) 3056-3061
53. Mannhaupt G., Schnall R., Karpov V., Vetter I., and Feldmann H. Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast. FEBS Letters 450 (1999) 27-34
54. Byrd C., Turner G.C., and Varshavsky A. The N-end rule pathway controls the import of peptides through degradation of a transcriptional repressor. EMBO J. 17 (1998) 269-277
55. Ptacek J., Devgan G., Michaud G., Zhu H., Zhu X., Fasolo J., et al. Global analysis of protein phosphorylation in yeast. Nature 438 (2005) 679-684
56. Manning G., Plowman G.D., Hunter T., and Sudarsanam S. Evolution of protein kinase signaling from yeast to man. Trends Biochem. Sci. 27 (2002) 514-520
57. Garten Y., Kaplan S., and Pilpel Y. Extraction of transcription regulatory signals from genome-wide DNA-protein interaction data. Nucl. Acids Res. 33 (2005) 605-615
58. Porter M.A., Mucha P.J., Newman M.E., and Warmbrand C.M. A network analysis of committees in the U.S. House of Representatives. Proc. Natl Acad. Sci. USA 102 (2005) 7057-7062
59. Shen-Orr S.S., Milo R., Mangan S., and Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genet. 31 (2002) 64-68