Single Cell Measurements and Stochastic Modeling of Intron Diffusion in HeLa Cells

Transcriptional bursting, transport, and degradation contribute to control the spatial and temporal abundances of RNA, affecting how RNA transfer information or perform regulatory functions. Several investigations have used single-molecule fluorescence in situ hybridization to explore endogenous transcription regulation in fixed cells, while others have used genetically engineered RNA-reporters and live-cell imaging to focus on intracellular diffusion. Fixed cell approaches hide direct temporal information, while reporter strains are expensive and may perturb natural processes. Here, we use an exogenous intron reporter system to measure RNA in both fixed and live cells and discover heterogeneous RNA diffusion patterns in single cells. We analyze a simple model of bursting and compartmental diffusion using Fisher Information and Chemical Master Equations to show that diffusion rates can be inferred from fixed cell measurements. Moreover, explicit consideration of diffusion can improve estimation of transcription regulation parameters. We then use simulations with known ground truth to show that parameters of reaction-diffusion processes can be recovered from single time point fixed-cell microscopy data. Finally, we infer a similar reaction diffusion model from fixed-cell experiments and validate our findings against live-cell time-lapse data.