High density simulation for transcriptional dynamics

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RNA polymerase II(RNAPII) is the responsible motor protein for transcription. Here we studied the formulation and results of a cellular automaton model of the RNAPII dynamics of gene transcription that takes account the effect of the velocity change according to the gene position, such as occurs in introns and exons. It was found that the RNAPII molecules move as a free-flow state, though regions of reduced velocity do exist such as exons, as far as the time interval between nearest RNAPII molecules is larger than the time required for an RNAPII passing the exclusion length in the velocity reduction region.