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Dynamic Modeling of mRNA Metabolism

Gene expression regulation is of vital importance for the functionality of the cell. Coordinated expression changes are crucial to the cell cycle, to environmental adaptations and to cell differentiation. In this project, we develop a new biochemical-bioinformatics approach for the measurement of the kinetic parameters of mRNA metabolism (i.e., RNA synthesis rate, nuclear and cytosolic degradation, and RNA export rate). Using RNA metabolic labeling in combination with deep sequencing (SLAM-Seq), we can distinguish transcripts that have been synthesized after the application of the labeling pulse from pre-existing ones. We analyze SLAM-Seq time series data for nuclear and cytosolic RNA by fitting a differential equation system with an appropriate statistical model.