A model of ribosome kinetics on dynamic mRNAs.

(A) The transcriptome in the model consists of two types of mRNAs: background mRNAs which are considered as monocistronic with no secondary structure, and dynamic mRNAs which are polycistronic with secondary structure. Initiation rates at potential start codons (green bars, with red bars indicating stop codons) can vary in dynamic mRNAs depending on the current structure around the translation initiation region (TIR) while they are modelled as fixed in the background mRNAs. The movement of the ribosome during elongation is illustrated. (B) The transcriptome is modelled using the framework of the stochastic model in [10], with added RNA folding reactions on the dynamic mRNA.