Abstract
We present a multi-site model describing the alternative use of the RNA splicing sites A3, A4, A5 and A7 in the human immunodeficiency virus HIV-1. Our goal is to integrate experimental data obtained on individual splicing sites into a global model of HIV-1 RNA alternative splicing. We give a qualitative validation of our model, and analyse the possible impact of variations of regulatory protein concentrations on virus multiplication.
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Bockmayr, A., Courtois, A.: Using hybrid concurrent constraint programming to model dynamic biological systems. In: Stuckey, P.J. (ed.) ICLP 2002. LNCS, vol. 2401, pp. 85–99. Springer, Heidelberg (2002)
Eveillard, D., Ropers, D., de Jong, H., Branlant, C., Bockmayr, A.: Multiscale modeling of alternative splicing regulation. In: Priami, C. (ed.) CMSB 2003. LNCS, vol. 2602, pp. 75–87. Springer, Heidelberg (2003)
Moore, M., Query, C., Sharp, P.: Splicing of precursors to messenger RNAs by the spliceosome. In: The RNA World, Cold Spring Harbor Laboratory Press (1993)
Smith, C.W., Valcarcel, J.: Alternative pre-mRNA splicing: the logic of combinatorial control. Trends In Biochemical Sciences 25(8), 381–388 (2000)
Purcell, D., Martin, M.: Alternative splicing of human immunodeficiency virus type 1 mRNA modulates viral protein expression, replication and infectivity. Journal of Virology 67(11), 6365–6378 (1993)
Hope, T.: The ins and outs of HIV rev. Arch. Biochem. Biophys. 365(2), 186–191 (1999)
O’Reilly, M., McNally, M., Beemon, K.: Two strong 5’ splice sites and competing, suboptimal 3’ splice sites involved in alternative splicing of human immunodeficiency virus type 1 RNA. Virology 213, 373–385 (1995)
Si, Z., Amendt, B.A., Stoltzfus, C.M.: Splicing efficiency of human immunodeficiency virus type 1 tat RNA is determined by both a suboptimal 3’ splice site and a 10 nucleotide exon splicing silencer element located within tat exon 2. Nucleic Acids Res. 25, 861–867 (1997)
Swanson, A.K., Stoltzfus, C.M.: Overlapping cis sites used for splicing of HIV-1 env/nef and rev mRNAs. J. Biol. Chem. 273, 34551–34557 (1998)
Schaal, H., Freund, M., Kammler, S., Asang, C., Caputi, M.: A bidirectional SR protein-dependent exonic splicing enhancer regulates rev, env, vpu and nef gene expression. In: Eukaryotic mRNA Processing (2003)
Gupta, V., Jagadeesan, R., Saraswat, V.: Computing with continuous change. Science of computer programming 30, 3–49 (1998)
Chabrier, N., Fages, F.: Symbolic model checking of biochemical networks. In: Priami, C. (ed.) CMSB 2003. LNCS, vol. 2602, pp. 149–162. Springer, Heidelberg (2003)
Pongoski, J., Asai, K., Cochrane, A.: Positive and negative modulation of human immunodeficiency virus type 1 Rev function by cis and trans regulators of viral RNA splicing. J. Virol. 76, 5108–5120 (2002)
Hammond, B.J.: Quantitative study of the control of HIV-1 gene expression. J. Theor. Biol. 163, 199–221 (1993)
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Bockmayr, A., Courtois, A., Eveillard, D., Vezain, M. (2005). Building and Analysing an Integrative Model of HIV-1 RNA Alternative Splicing. In: Danos, V., Schachter, V. (eds) Computational Methods in Systems Biology. CMSB 2004. Lecture Notes in Computer Science(), vol 3082. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-25974-9_5
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DOI: https://doi.org/10.1007/978-3-540-25974-9_5
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