A multi-scale constraint programming model of alternative splicing regulation

Authors:
Damien Eveillard;Delphine Ropers;Hidde de Jong;Christiane Branlant;Alexander Bockmayr
Affiliations:
LORIA, Université Henri Poincaré, BP 239, 54506 Vandoeuvre-lès-Nancy, France and Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 CNRS-UHP, BP 239, 54506 ...;Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 CNRS-UHP, BP 239, 54506 Vandoeuvre-lès-Nancy, France;INRIA Rhòne-Alpes, Helix Project, 655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier, France;Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 CNRS-UHP, BP 239, 54506 Vandoeuvre-lès-Nancy, France;LORIA, Universitè Henri Poincaré, BP 239, 54506 Vandoeuvre-lès-Nancy, France
Venue:
Theoretical Computer Science - Special issue: Computational systems biology
Year:
2004

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Abstract

Alternative splicing is a key process in post-transcriptional regulation, by which different mature RNA can be obtained from the same premessenger RNA. The resulting combinatorial complexity contributes to biological diversity, especially in the case of the human immunodeficiency virus HIV-1. Using a constraint programming approach, we develop a model of the alternative splicing regulation in HIV-1. Our model integrates different scales (single site vs. multiple sites), and thus allows us to exploit several types of experimental data available to us.