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bioRxiv · 10.1101/825869

Stochastic simulation platform for visualization and estimation of transcriptional kinetics

Gorin, G.·Wang, M.·Golding, I.·Xu, H.
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Abstract

We present an implementation of the Gillespie algorithm that simulates the stochastic kinetics of nascent and mature RNA. Our model includes two-state gene regulation, RNA synthesis initiation and stepwise elongation, release to the cytoplasm, and stepwise degradation, a granular description currently tractable only by simulation. To facilitate comparison with experimental data, the algorithm predicts fluorescent probe signals measurable by single-cell RNA imaging. We approach the inverse problem of estimating underlying parameters in a five-dimensional parameter space and suggest optimization heuristics that successfully recover known reaction rates from simulated gene expression turn-on data. The simulation framework includes a graphical user interface, available as a MATLAB app at https://data.caltech.edu/records/1287.

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Gorin, G., Wang, M., Golding, I., Xu, H.. 2019-11-02. Stochastic simulation platform for visualization and estimation of transcriptional kinetics. https://doi.org/10.1101/825869

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