Stochastic effects of multiple regulators on expression profiles in eukaryotes

Journal of Theoretical Biology

Volumn 233, Issue 3, 2005, Pages 423-433

  Paszek, Pawel ^a   Lipniacki, Tomasz ^a,b,d   Brasier, Allan R ^c   Tian, Bing ^c   Nowak, David E ^c   Kimmel, Marek ^a  

^a Rice University   (United States)

^b INSTITUTE OF FUNDAMENTAL TECHNOLOGICAL RESEARCH   (Poland)

^c University of Texas Medical Branch School of Medicine   (United States)

^d UNIVERSITY OF TEXAS MEDICAL BRANCH   (United States)

Author keywords

Expression profiles; NF B; Single cell simulations; Stochastic gene regulation

Indexed keywords

IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; TUMOR NECROSIS FACTOR ALPHA;

EUKARYOTE; GENE EXPRESSION; STOCHASTICITY;

ARTICLE; CELL POPULATION; EUKARYOTE; GENE CONTROL; GENE EXPRESSION; GENETIC TRANSCRIPTION; HELA CELL; PRIORITY JOURNAL; STOCHASTIC MODEL;

ANIMALS; CELL PHYSIOLOGY; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENE SILENCING; MODELS, GENETIC; TRANSCRIPTION, GENETIC;

EUKARYOTA;

EID: 11844251994     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jtbi.2004.10.023     Document Type: Article

References (19)

1. G.K. Ackers, A.D. Johnson, and M.A. Shea Quantitative model for gene regulation by λ phage repressor Proc. Natl Acad. Sci. USA 79 1982 1129 1133
2. C. Blattner, P. Kannouche, M. Litfin, K. Bender, H.J. Rahmsdorf, J.F. Angulo, and P. Herrlich UV-induced stabilization of c-fos and other short-lived mRNAs Mol. Cell. Biol. 20 2000 3616 3625
3. A. Eberharter, and P.B. Becker Histone acetylation a switch between repressive and permissive chromatin EMBO Rep. 3 2002 224 229
4. A.M. Femino, F.S. Fay, K. Fogarty, and R.H. Singer Visualization of single RNA transcripts in situ Science 280 1998 585 590
5. P.D. Gregory, K. Wagner, and W. Hörz Histone acetylation and chromatin remodeling Exp. Cell Res. 265 2001 195 202
6. A.D. Johnson, B.J. Meyer, and M. Ptashne Interactions between DNA-bound repressors govern regulation by the λ phage repressor Proc. Natl Acad. Sci. USA 76 1979 5061 5065
7. T.B. Kepler, and T.C. Elston Stochasticity in transcriptional regulation orgins, consequences, and mathematical representations Biophys. J. 81 2001 3116 3136
8. M.S.H. Ko A stochastic model for gene induction J. Theor. Biol. 153 1991 181 194
9. M.S.H. Ko Induction mechanism of a single gene molecule stochastic or deterministic? Bioassays 14 5 1992 341 346
10. M.S.H. Ko, H. Nakauchi, and N. Takahashi The dose dependence of glucocorticoid-inducible gene expression results from changes in the number of transcriptionally active templates EMBO J. 9 9 1990 2835 2842
11. T. Lipniacki, P. Paszek, A.R. Brasier, B. Luxon, and M. Kimmel Mathematical model of NF-κB module J. Theor. Biol. 228 2004 195 215 (doi:10.1016/j.jtbi.2004.01.001)
12. M. Louis, L. Holm, L. Sanchez, and M. Kaufman A theoretical model for the regulation of sex-lethal, a gene that controls sex determination and dosage compensation in Drosophila melanogaster Genetics 165 2003 1355 1384
13. H.H. McAdams, and A. Arkin Stochastic mechanisms in gene expression Proc. Natl Acad. Sci. USA 94 1997 814 819
14. G. Nelson, L. Paraoan, D.G. Spiller, G.J.C. Wilde, A.M. Browne, P.K. Djali, J.F. Unitt, E. Sullivan, E. Floettmann, and M.R.H. White Multi-parameter analysis of the kinetics of NF-κB signaling and transcription in single living cells J. Cell Sci. 115 2002 1137 1148
15. Nowak, D., E., 2004. Unpublished data.
16. J.R. Pirone, and T.C. Elston Fluctuations in transcription factor binding can explain the graded and binary responses observed in inducible gene expression J. Theor. Biol. 226 2004 111 121 (doi:10.1016/j.jtbi.2003.08.008)
17. B. Tian, and A.R. Brasier Identification of a nuclear factor kappa B-dependent gene network Recent Progr. Hormone Res. 58 2003 95 130
18. B. Tian, Y. Zhang, B.A. Luxon, R.P. Garofalo, A. Casola, M. Sinha, and A.R. Brasier Identification of NF-κB-dependent gene networks in respiratory syncytial virus-infected cells J. Virol. 76 2002 6800 6814
19. A.P. Wolfe, and D. Pruss Targeting chromatin disruption transcription regulators that acetylate histones Cell 84 1996 817 819