Information theory, gene expression, and combinatorial regulation: a quantitative analysis
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According to a functional definition of the term “gene”, a protein-coding gene corresponds to a polypeptide and, hence, a coding sequence. It is therefore as such not yet present at the DNA level, but assembled from possibly heterogeneous pieces in the course of RNA processing. Assembly and regulation of genes require, thus, information about when and in which quantity specific polypeptides are to be produced. To assess this, we draw upon precise biochemical data. On the basis of our conceptual framework, we also develop formal models for the coordinated expression of specific sets of genes through the interaction of transcripts and mRNAs and with proteins via a precise putative regulatory code. Thus, the nucleotides in transcripts and mRNA are not only arranged into amino acid-coding triplets, but at the same time may participate in regulatory oligomotifs that provide binding sites for specific proteins. We can then quantify and compare product and regulatory information involved in gene expression and regulation.
KeywordsGene expression Gene regulation RNA Combinatorial regulation scheme Information theory
We thank our colleagues, who contributed by discussion over the years to evolution of the ideas presented here, and in particular Manfred Eigen and the participants of the Klosters Winter Seminar. We thank the three referees for their insightful comments. The second author was supported by the French CNRS, the Universities Paris 6 and 7, and by bioMérieux SA, in particular by Dr. Alain Mérieux. He also thanks the Max Planck Institute for Mathematics in the Sciences for its hospitality and good working conditions.
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