Fine tuning gene expression through short DNA-protein binding cycles

Biochimie

Volumn 91, Issue 7, 2009, Pages 933-941

  Michel, Denis ^a  

^a UNIVERSITÉ DE RENNES 1   (France)

Author keywords

Determinism; Differential dynamics; Ergodicity; Single cell; Stochasticity

Indexed keywords

DNA; PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; CHROMATIN; GENE EXPRESSION; GENE EXPRESSION PROFILING; IN VITRO STUDY; MATHEMATICAL ANALYSIS; PROMOTER REGION; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; QUANTITATIVE ANALYSIS; TRANSCRIPTION INITIATION;

ANIMALS; BINDING SITES; DNA; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION; HUMANS; TRANSCRIPTION FACTORS;

EID: 67349180635     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2009.03.022     Document Type: Article

References (39)

1. Meijsing S.H., Elbi C., Luecke H.F., Hager G.L., and Yamamoto K.R. The ligand binding domain controls glucocorticoid receptor dynamics independent of ligand release. Mol. Cell. Biol. 27 (2007) 2442-2451
2. Sharp Z.D., Mancini M.G., Hinojos C.A., Dai F., Berno V., Szafran A.T., Smith K.P., Lele T.P., Ingber D.E., and Mancini M.A. Estrogen-receptor-alpha exchange and chromatin dynamics are ligand- and domain-dependent. J. Cell. Sci. 119 (2006) 4101-4116
3. Bosisio D., Marazzi I., Agresti A., Shimizu N., Bianchi M.E., and Natoli G. A hyper-dynamic equilibrium between promoter-bound and nucleoplasmic dimers controls NF-kappaB-dependent gene activity. EMBO J. 25 (2006) 798-810
4. Sprouse R.O., Karpova T.S., Mueller F., Dasgupta A., McNally J.G., and Auble D.T. Regulation of TATA-binding protein dynamics in living yeast cells. Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 13304-13308
5. Freeman B.C., and Yamamoto K.R. Continuous recycling: a mechanism for modulatory signal transduction, Trends. Biochem. Sci. 26 (2001) 285-290
6. Muldrow T.A., Campbell A.M., Weil P.A., and Auble D.T. MOT1 can activate basal transcription in vitro by regulating the distribution of TATA binding protein between promoter and nonpromoter sites. Mol. Cell. Biol. 19 (1999) 2835-2845
7. Sprague B.L., Pego R.L., Stavreva D.A., and McNally J.G. Analysis of binding reactions by fluorescence recovery after photobleaching. Biophys. J. 86 (2004) 3473-3495
8. Ko M.S.H. A stochastic model for gene induction. J. Theor. Biol. 153 (1991) 181-194
9. Van Kampen N.G. Stochastic Processes in Physics and Chemistry. third ed. (2007), Elsevier, North-Holland, Amsterdam
10. Paulsson J., Berg O.G., and Ehrenberg M. Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 7148-7153
11. Kepler T.B., and Elston T.C. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. Biophys. J. 81 (2001) 3116-3136
12. Pedraza J.M., and Paulsson J. Effects of molecular memory and bursting on fluctuations in gene expression. Science 319 (2008) 339-343
13. Raj A., and van Oudenaarden A. Nature nurture, or chance: stochastic gene expression and its consequences. Cell 135 (2008) 216-226
14. Ackers G.K., Johnson A.D., and Shea M.A. Quantitative model for gene regulation by lambda phage repressor. Proc. Natl. Acad. Sci. U.S.A. 79 (1982) 1129-1133
15. Biot J.B. Méthodes mathématiques et expérimentales pour discerner les mélanges et les combinaisons chimiques. Mem. Acad. Sci. 15 (1838) 93-279
16. Berg O.G., and Blomberg C. Mass action relations in vivo with application to the lac operon. J. Theor. Biol. 67 (1977) 523-533
17. Chu D., Radu Zabet N., and Mitavskiy B. Models of transcription factor binding: sensitivity of activation functions to model assumptions. J. Theor. Biol. 257 (2009) 419-429
18. Lebrecht D., Foehr M., Smith E., Lopes F.J.P., Vanario-Alonso C.E., Reinitz J., Burz D.S., and Hanes S.D. Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila. Proc. Natl. Acad. Sci. U.S.A. (2005) 13176-13181
19. Ko M.S.H., Nakauchi H., and Naomi Takahashi N. The dose dependence of glucocorticoid-inducible gene expression results from changes in the number of transcriptionally active templates. EMBO J. 9 (1990) 2835-2842
20. Elowitz M.B., Levine A.J., Siggia E.D., and Swain P.S. Stochastic gene expression in a single cell. Science 297 (2002) 1183-1186
21. Zhang J., Xu F., Hashimshony T., Keshet I., and Cedar H. Establishment of transcriptional competence in early and late S phase. Nature 420 (2002) 198-202
22. van Slyke D., and Cullen G.E. The mode of action of urease and of enzymes in general. J. Biol. Chem. 19 (1914) 141-180
23. Fletcher T.M., Xiao N., Mautino G., Baumann C.T., Wolford R., Warren B.S., and Hager G.L. ATP-dependent mobilization of the glucocorticoid receptor during chromatin remodeling. Mol. Cell. Biol. 22 (2002) 3255-3263
24. Molinari E., Gilman M., and Natesan S. Proteasome-mediated degradation of transcriptional activators correlates with activation domain potency in vivo. EMBO J. 18 (1999) 6439-6447
25. Freeman B.C., and Yamamoto K.R. Disassembly of transcriptional regulatory complexes by molecular chaperones. Science 296 (2002) 2232-2235
26. Wochnik G.M., Young J.C., Schmidt U., Holsboer F., Hartl F.U., and Rein T. Inhibition of GR-mediated transcription by p23 requires interaction with Hsp90. FEBS Lett. 560 (2004) 35-38
27. Sangster T.A., Salathia N., Undurraga S., Milo R., Schellenberg K., Lindquist S., and Queitsch C. HSP90 affects the expression of genetic variation and developmental stability in quantitative traits. Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 2963-2968
28. Blake W.J., Balázsi G., Kohanski M.A., Isaacs F.J., Murphy K.F., Kuang Y., Cantor C.R., Walt D.R., and Collins J.J. Phenotypic consequences of promoter-mediated transcriptional noise. Mol. Cell. 24 (2006) 853-865
29. Fried M.G., and Liu G. Molecular sequestration stabilizes CAP-DNA complexes during polyacrylamide gel electrophoresis. Nucleic Acids Res. 22 (1994) 5054-5059
30. Choi P.J., Cai L., Frieda K., and Xie X.S. A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 322 (2008) 442-446
31. Lu H.P., Xun L., and Xie X.S. Single-molecule enzymatic dynamics. Science 282 (1998) 1877-1882
32. English B.P., Min W., van Oijen A.M., Lee K.T., Luo G., Sun H., Cherayil B.J., Kou S.C., and Xie X.S. Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited. Nat. Chem. Biol. 2 (2006) 87-94
33. Min W., Gopich I.V., English B.P., Kou S.C., Xie X.S., and Szabo A. When does the Michaelis-Menten equation hold for fluctuating enzymes?. J. Phys. Chem. B 110 (2006) 20093-20097
34. Agresti A., Scaffidi P., Riva A., Caiolfa V.R., and Bianchi M.E. GR and HMGB1 interact only within chromatin and influence each other's residence time. Mol. Cell 18 (2005) 109-121
35. Nagaich A.K., Walker D.A., Wolford R., and Hager G.L. Rapid periodic binding and displacement of the glucocorticoid receptor during chromatin remodeling. Mol. Cell 14 (2004) 163-174
36. Métivier R., Penot G., Hübner M.R., Reid G., Brand H., Kos M., and Gannon F. Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115 (2003) 751-763
37. Kou S.C., Cherayil B.J., Min W., English B.P., and Xie X.S. Single-molecule Michaelis-Menten equations. J. Phys. Chem. B 109 (2005) 19068-19081
38. Chang H.H., Hemberg M., Barahona M., Ingber D.E., and Huang S. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature 453 (2008) 544-547
39. Becskei A., and Serrano L. Engineering stability in gene networks by autoregulation. Nature 405 (2000) 590-593