Abstract
Gene expression relies on the interaction of numerous transcriptional signals at the promoter to elicit a response—to read or not to read the genomic code, and if read, the strength of the read. The interplay of transcription factors can be viewed as nonlinear dynamics underlying the biological complexity. Here we analyse the regulation of the cyclooxygenase 2 promoter by NF-κB using thermostatistical and quantitative kinetic modelling and propose the presence of a genetic Boolean AND logic gate controlling the differential expression of cyclooxygenase 2 among species.
Keywords
- Histone Methylation
- Nonlinear Regulation
- COX2 Promoter
- Transcription Factor Nuclear Factor
- Degeneracy Factor
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
This is a preview of subscription content, access via your institution.
Buying options
References
Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., et al.: The sequence of the human genome. Science 291, 1304–1351 (2001)
Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., et al.: Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)
Okamoto, A., Tanaka, K., Saito, I.: DNA logic gates. J. Am. Chem. Soc. 126, 9458–9463 (2004)
Goldman, N., Bertone, P., Chen, S., Dessimoz, C., LeProust, E.M., et al.: Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature 494, 77–80 (2013)
Fisher, J., Henzinger, T.A.: Executable cell biology. Nat. Biotechnol. 25, 1239–1249 (2007)
Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G., et al.: The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390, 249–256 (1997)
Gibson, D.G., Glass, J.I., Lartigue, C., Noskov, V.N., Chuang, R.Y., et al.: Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52–56 (2010)
Wan, F., Lenardo, M.J.: Specification of DNA binding activity of NF-kappaB proteins. Cold Spring Harb. Perspect. Biol. 1, a000067 (2009)
Wong, D., Teixeira, A., Oikonomopoulos, S., Humburg, P., Lone, I.N., et al.: Extensive characterization of NF-kappaB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. Genome Biol. 12, R70 (2011)
Fedorova, L., Fedorov, A.: Introns in gene evolution. Genetica 118, 123–131 (2003)
Matlin, A.J., Clark, F., Smith, C.W.: Understanding alternative splicing: towards a cellular code. Nat. Rev. Mol. Cell Biol. 6, 386–398 (2005)
Black, D.L.: Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72, 291–336 (2003)
Modrek, B., Lee, C.: A genomic view of alternative splicing. Nat. Genet. 30, 13–19 (2002)
Mockler, T.C., Chan, S., Sundaresan, A., Chen, H., Jacobsen, S.E., et al.: Applications of DNA tiling arrays for whole-genome analysis. Genomics 85, 1–15 (2005)
Wang, Z., Gerstein, M., Snyder, M.: RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63 (2009)
Cavadas, M.A.S., Cheong, A.: Monitoring of transcriptional dynamics of HIF and NF kappa B activities. Bioluminescent Imaging Methods Protoc. 1098, 97–105 (2014)
Carey, M., Lin, Y.S., Green, M.R., Ptashne, M.: A mechanism for synergistic activation of a mammalian gene by GAL4 derivatives. Nature 345, 361–364 (1990)
Bruning, U., Fitzpatrick, S.F., Frank, T., Birtwistle, M., Taylor, C.T., et al.: NFkappaB and HIF display synergistic behaviour during hypoxic inflammation. Cell. Mol. Life Sci. 69, 1319–1329 (2012)
Rossi, F.M., Kringstein, A.M., Spicher, A., Guicherit, O.M., Blau, H.M.: Transcriptional control: rheostat converted to on/off switch. Mol. Cell 6, 723–728 (2000)
Nguyen, L.K., Cavadas, M.A., Kholodenko, B.N., Frank, T.D., Cheong, A.: Species differential regulation of COX2 can be described by an NFkappaB-dependent logic AND gate. Cell. Mol. Life Sci. 72, 2431–2443 (2015)
Biggar, S.R., Crabtree, G.R.: Cell signaling can direct either binary or graded transcriptional responses. EMBO J. 20, 3167–3176 (2001)
Joers, A., Jaks, V., Kase, J., Maimets, T.: p53-dependent transcription can exhibit both on/off and graded response after genotoxic stress. Oncogene 23, 6175–6185 (2004)
Ertel, A., Tozeren, A.: Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality. BMC Genom. 9, 628 (2008)
Ertel, A., Tozeren, A.: Switch-like genes populate cell communication pathways and are enriched for extracellular proteins. BMC Genom. 9, 3 (2008)
Nguyen, L.K., Cavadas, M.A., Scholz, C.C., Fitzpatrick, S.F., Bruning, U., et al.: A dynamic model of the hypoxia-inducible factor 1-alpha (HIF-1alpha) network. J. Cell Sci. 126, 1454–63 (2013)
Leung, T.H., Hoffmann, A., Baltimore, D.: One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers. Cell 118, 453–464 (2004)
Li, J., Schmidt, A.M.: Characterization and functional analysis of the promoter of RAGE, the receptor for advanced glycation end products. J. Biol. Chem. 272, 16498–16506 (1997)
Ohmori, Y., Hamilton, T.A.: Cooperative interaction between interferon (IFN) stimulus response element and kappa B sequence motifs controls IFN gamma- and lipopolysaccharide-stimulated transcription from the murine IP-10 promoter. J. Biol. Chem. 268, 6677–6688 (1993)
Fiering, S., Northrop, J.P., Nolan, G.P., Mattila, P.S., Crabtree, G.R., et al.: Single cell assay of a transcription factor reveals a threshold in transcription activated by signals emanating from the T-cell antigen receptor. Genes Dev. 4, 1823–1834 (1990)
Lin, Y.S., Carey, M., Ptashne, M., Green, M.R.: How different eukaryotic transcriptional activators can cooperate promiscuously. Nature 345, 359–361 (1990)
Weintraub, H.: Assembly and propagation of repressed and depressed chromosomal states. Cell 42, 705–711 (1985)
Santos-Rosa, H., Schneider, R., Bannister, A.J., Sherriff, J., Bernstein, B.E., et al.: Active genes are tri-methylated at K4 of histone H3. Nature 419, 407–411 (2002)
Margueron, R., Trojer, P., Reinberg, D.: The key to development: interpreting the histone code? Curr. Opin. Genet. Dev. 15, 163–176 (2005)
Kurdistani, S.K.: Histone modifications as markers of cancer prognosis: a cellular view. Br. J. Cancer 97, 1–5 (2007)
Nguyen, L.K., Munoz-Garcia, J., Maccario, H., Ciechanover, A., Kolch, W., et al.: Switches, excitable responses and oscillations in the Ring1B/Bmi1 ubiquitination system. PLoS Comput. Biol. 7, e1002317 (2011)
Seok, J., Warren, H.S., Cuenca, A.G., Mindrinos, M.N., Baker, H.V., et al.: Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc. Natl. Acad. Sci. U. S. A. 110, 3507–3512 (2013)
Cheng, Y., Ma, Z., Kim, B.H., Wu, W., Cayting, P., et al.: Principles of regulatory information conservation between mouse and human. Nature 515, 371–375 (2014)
Lin, S., Lin, Y., Nery, J.R., Urich, M.A., Breschi, A., et al.: Comparison of the transcriptional landscapes between human and mouse tissues. Proc. Natl. Acad. Sci. U. S. A. 111, 17224–17229 (2014)
Wittkopp, P.J., Kalay, G.: Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat. Rev. Genet. 13, 59–69 (2012)
Ackers, G.K., Johnson, A.D., Shea, M.A.: Quantitative model for gene regulation by lambda phage repressor. Proc. Natl. Acad. Sci. U. S. A. 79, 1129–1133 (1982)
Wang, J., Ellwood, K., Lehman, A., Carey, M.F., She, Z.S.: A mathematical model for synergistic eukaryotic gene activation. J. Mol. Biol. 286, 315–325 (1999)
Buchler, N.E., Gerland, U., Hwa, T.: On schemes of combinatorial transcription logic. Proc. Natl. Acad. Sci. U. S. A. 100, 5136–5141 (2003)
Segal, E., Raveh-Sadka, T., Schroeder, M., Unnerstall, U., Gaul, U.: Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 451, 535–540 (2008)
Dresch, J.M., Liu, X., Arnosti, D.N., Ay, A.: Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects. BMC Syst. Biol. 4, 142 (2010)
Frank, T.D., Carmody, A.M., Kholodenko, B.N.: Versatility of cooperative transcriptional activation: a thermodynamical modeling analysis for greater-than-additive and less-than-additive effects. PLoS One 7, e34439 (2012)
Shea, M.A., Ackers, G.K.: The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. J. Mol. Biol. 181, 211–230 (1985)
Frank, T.D., Cheong, A., Okada-Hatakeyama, M., Kholodenko, B.N.: Catching transcriptional regulation by thermostatistical modeling. Phys. Biol. 9, 045007 (2012)
Bintu, L., Buchler, N.E., Garcia, H.G., Gerland, U., Hwa, T., et al.: Transcriptional regulation by the numbers: applications. Curr. Opin. Genet. Dev. 15, 125–135 (2005)
Bintu, L., Buchler, N.E., Garcia, H.G., Gerland, U., Hwa, T., et al.: Transcriptional regulation by the numbers: models. Curr. Opin. Genet. Dev. 15, 116–124 (2005)
Kulasiri, D., Nguyen, L.K., Samarasinghe, S., Xie, Z.: A review of systems biology perspective on genetic regulatory networks with examples. Curr. Bioinform. 3, 197–225 (2008)
Smolen, P., Baxter, D.A., Byrne, J.H.: Modeling transcriptional control in gene networks–methods, recent results, and future directions. Bull. Math. Biol. 62, 247–292 (2000)
De Jong, H.: Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 9, 67–103 (2002)
Chen, T., He, H.L., Church, G.M.: Modeling gene expression with differential equations. Pac. Symp. Biocomput. 4, 29–40 (1999)
Babu, M.M., Luscombe, N.M., Aravind, L., Gerstein, M., Teichmann, S.A.: Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol. 14, 283–291 (2004)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Frank, T.D., Cavadas, M.A.S., Nguyen, L.K., Cheong, A. (2016). Non-linear Dynamics in Transcriptional Regulation: Biological Logic Gates. In: Carballido-Landeira, J., Escribano, B. (eds) Nonlinear Dynamics in Biological Systems. SEMA SIMAI Springer Series, vol 7. Springer, Cham. https://doi.org/10.1007/978-3-319-33054-9_3
Download citation
DOI: https://doi.org/10.1007/978-3-319-33054-9_3
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-33053-2
Online ISBN: 978-3-319-33054-9
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)