Network motifs: Structure does not determine function

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Ingram, Piers J ^a   Stumpf, Michael P H ^a   Stark, Jaroslav ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; REPRESSOR PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN; TRANSCRIPTION FACTOR;

ANALYTICAL PARAMETERS; ARTICLE; ARTIFICIAL NEURAL NETWORK; BINDING KINETICS; CONTROLLED STUDY; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; NONHUMAN; PROMOTER REGION; SACCHAROMYCES CEREVISIAE; STRUCTURE ACTIVITY RELATION; TIME SERIES ANALYSIS; TRANSCRIPTION REGULATION;

AMINO ACID MOTIFS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; MODELS, BIOLOGICAL; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION, GENETIC;

SACCHAROMYCES CEREVISIAE;

EID: 33745780500     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-108     Document Type: Article

References (41)

1. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U: Network motifs: simple building blocks of complex networks. Science 2002, 298(5594):824-827.
2. Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S, Ayzenshtat I, Sheffer M, Alon U: Superfamilies of evolved and designed networks. Science 2004,303(5663):1538-1542.
3. Prill R, Iglesias P, Levchenko A: Dynamic Properties of Network Motifs Contribute to Biological Network Organization. PLoS Biol 2005, 3 (11):e343.
4. Mangan S, Alon U: Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A 2003, 100(21):11980-11985.
5. Hayot F, Jayaprakash C: A feedforward loop motif in transcriptional regulation: induction and repression. J Theor Bio 2005, 234:133-143.
6. Mangan S, Zaslaver A, Alon U: The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J Mol Biol 2003, 334(2):197-204.
7. Artzy-Randrup Y, Fleishman SJ, Ben-Tal N, Stone L: Comment on "Network motifs: simple building blocks of complex networks" and "Superfamilies of evolved and designed networks". Science 2004, 305(5687):1107.
8. Huang S: Back to the biology in systems biology: what can we learn from biomolecular networks? Brief Fund Genomic Proteomic 2004, 2(4):279-297.
9. Conant GC, Wagner A: Convergent evolution of gene circuits. Nat Genet 2003, 34(3):264-266.
10. Gillespie D: Exact stochastic simulation of coupled chemical reactions. J Phys Chem 1977, 81:2340-2361.
11. Ogden SK, Lee KC, Wernke-Dollries K, Stratton SA, Aronow B, Barton MC: p53 targets chromatin structure alteration to repress alpha-fetoprotein gene expression. J Biol Chem 2001, 276(45):42057-42062.
12. Hiroi H, Christenson LK, Chang L, Sammel MD, Berger SL, Strauss JFr: Temporal and spatial changes in transcription factor binding and histone modifications at the steroidogenic acute regulatory protein (stAR) locus associated with stAR transcription. Mol Endocrinol 2004, 18(4):791-806.
13. Cosma MP: Ordered recruitment: gene-specific mechanism of transcription activation. Mol Cell 2002, 10(2):227-236.
14. Bundschuh R, Hayot F, Jayaprakash C: The role of dimerization in noise reduction of simple genetic networks. J Theor Biol 2003, 220(2):261-269.
15. Ptashne M, Jeffrey A, Johnson AD, Maurer R, Meyer BJ, Pabo CO, Roberts TM, Sauer RT: How the lambda repressor and cro work. Cell 1980, 19:1-11.
16. Mai B, Breeden L: CLNI and its repression by Xbp I are important for efficient sporulation in budding yeast. Mol Cell Biol 2000, 20(2):478-487.
17. Althoefer H, Schleiffer A, Wassmann K, Nordheim A, Ammerer G: Mcm l is required to coordinate G2-specific transcription in Saccharomyces cerevisiae. Mol Cell Biol 1995, 15(11):S917-S928.
18. Kratzer S, Schuller HJ: Transcriptional control of the yeast acetyl-CoA synthetase gene, ACSI, by the positive regulators CAT8 and ADRI and the pleiotropic repressor UME6. Mol Microbiol 1997, 26(4):631-641.
19. Kratzer S, Schuller HJ: Carbon source-dependent regulation of the acetyl-coenzyme A synthetase-encoding gene ACSI from Saccharomyces cerevisiae. Gene 1995, 161:75-79.
20. Schuller HJ, Schutz A, Knab S, Hoffmann B, Schweizer E: Importance of general regulatory factors Raplp, Abfl p and Rebl p for the activation of yeast fatty acid synthase genes FAS1 and FAS2. Eur J Biochem 1994, 225:213-222.
21. Herrero P, Flores L, de la Cera T, Moreno F: Functional characterization of transcriptional regulatory elements in the upstream region of the yeast GLKI gene. Biochem J 1999, 343(Pt 2):319-325.
22. Moreno-Herrero F, Herrero P, Colchero J, Baro AM, Moreno F: Analysis by atomic force microscopy of Med8 binding to cis-acting regulatory elements of the SUC2 and HXK2 genes of saccharomyces cerevisiae. FEBS Lett 1999, 459(3):427-432.
23. Bu Y, Schmidt MC: Identification of cis-acting elements in the SUC2 promoter of Saccharomyces; cerevisiae required for activation of transcription. Nucleic Acids Res 1998, 26(4):1002-1009.
24. Estruch F, Carlson M: Two homologous zinc finger genes identified by multicopy suppression in a SNFI protein kinase mutant of Saccharomyces cerevisiae. Mol Cell Biol 1993, 13(7):3872-3881.
25. Nehlin JO, Carlberg M, Ronne H: Yeast SKOI gene encodes a bZIP protein that binds to the CRE motif and acts as a repressor of transcription. Nucleic Acids Res 1992, 20(20):5271-5278.
26. Coffman JA, Rai R, Loprete DM, Cunningham T, Svetlov V, Cooper TG: Cross regulation of four GATA factors that control nitrogen catabolic gene expression in Saccharomyces cerevisiae. J. Bacteriol 1997, 179(11):3416-3429.
27. Cunningham TS, Svetlov W, Rai R, Smart W, Cooper TG: GIn3p is capable of binding to UAS(NTR) elements and activating transcription in Saccharomyces cerevisiae. J Bacterial 1996, 178(12):3470-3479.
28. Talibi D, Grenson M, Andre B: Cis- and trans-acting elements determining induction of the genes of the gamma-aminobutyrate (GABA) utilization pathway in Saccharomyces; cerevisiae. Nucleic Acids Res 1995, 23(4):550-557.
29. Andre B, Talibi D, Soussi Boudekou S, Hein C, Vissers S, Coornaert D: Two mutually exclusive regulatory systems inhibit UASGATA, a cluster of 5'-GAT(A/T)A-3' upstream from the UGA4 gene of Saccharomyces cerevisiae. Nucleic Acids Res 1995,23(4):558-564.
30. Cunningham TS, Cooper TG: The Saccharomyces cerevisiae DAL80 repressor protein binds to multiple copies of GATAA-containing sequences (URSGATA). J Bacteriol 1993, 175(18):5851-5861.
31. Proft M, Serrano R: Repressors and upstream repressing sequences of the stress-regulated ENAI gene in Saccharomyces cerevisiae: bZIP protein Sko l p confers HOG-dependent osmotic regulation. Mol Cell Biol 1999, 19:537-546.
32. Huie MA, Scott EW, Drazinic CM, Lopez MC, Hornstra IK, Yang TP, Baker HV: Characterization of the DNA-binding activity of GCRI: in vivo evidence for two GCRI-binding sites in the upstream activating sequence of TPI of Saccharomyces cerevisiae. Mol Cell Biol 1992, 12(6):2690-2700.
33. Brindle PK, Holland JP, Willett CE, Innis MA, Holland MJ: Multiple factors bind the upstream activation sites of the yeast enolase genes ENO1 and EN02: ABFI protein, like repressor activator protein RAP1, binds cis-acting sequences which modulate repression or activation of transcription. Mol Cell Biol 1990, 10(9):4872-4885.
34. Machida M, Jigami Y, Tanaka H: Purification and characterization of a nuclear factor which binds specifically to the upstream activation sequence of Saccharomyces cerevisiae enolase l gene. Eur J Biochem 1989, 184(2):305-311.
35. Machida M, Uemura H, Jigami Y, Tanaka H: The protein factor which binds to the upstream activating sequence of Saccharomyces cerevisiae ENO1 gene. Nucleic Acids Res 1988, 16(4):1407-1422.
36. Willett CE, Gelfman CM, Holland MJ:. A complex regulatory element from the yeast gene EN02 modulates GCRI-dependent transcriptional activation. Mol Cell Biol 1993, 13(4).2623-2633.
37. Holland JP, Brindle PK, Holland MJ: Sequences within an upstream activation site in the yeast enolase gene EN02 modulate repression of ENO2 expression in strains carrying a null mutation in the positive regulatory gene GCRI. Mol Cell Biol 1990,10(9):4863-4871.
38. Zaragoza O, Vincent O, Gancedo JM: Regulatory elements in the FBPI promoter respond differently to glucose-dependent signals in Saccharomyces cerevisiae. Biochem J 2001, 359(Pt 1): 193-201.
39. Vincent O, Carlson M: Sip4, a Snfl kinase-dependent transcriptional activator, binds to the carbon source-responsive element of gluconeogenic genes. EMBO J 1998,17(23):7002-7008.
40. Scholer A, Schuller HJ: A carbon source-responsive promoter element necessary for activation of the isocitrate lyase gene ICLI is common to genes of the gluconeogenic pathway in the yeast Saccharomyces cerevisiae. Mol Cell Biol 1994, 14(6):3613-3622.
41. Roth S, Schuller HJ: Cat8 and Sip4 mediate regulated transcriptional activation of the yeast malate dehydrogenase gene MDH2 by three carbon source-responsive promoter elements. Yeast 2001, 18(2):151-162.