Path-preference cellular-automaton model for traffic flow through transit points and its application to the transcription process in human cells

摘要

We all use path routing everyday as we take shortcuts to avoid traffic jams, or by using faster traffic means.nPrevious models of traffic flow of RNA polymerase II (RNAPII) during transcription, however, were restrictednto one dimension along the DNA template. Here we report the modeling and application of traffic flow inntranscription that allows preferential paths of different dimensions only restricted to visit some transit points,nas previously introduced between the 5u0002 and 3u0002 end of the gene. According to its position, an RNAPII proteinnmolecule prefers paths obeying two types of time-evolution rules. One is an asymmetric simple exclusion processn(ASEP) along DNA, and the other is a three-dimensional jump between transit points in DNA where RNAPIIs arenstaying. Simulations based on our model, and comparison experimental results, reveal how RNAPII molecules arendistributed at the DNA-loop-formation-related protein binding sites as well as CTCF insulator proteins (or exons).nAs time passes after the stimulation, the RNAPII density at these sites becomes higher. Apparent far-distancenjumps in one dimension are realized by short-range three-dimensional jumps between DNA loops. We confirmnthe above conjecture by applying our model calculation to the SAMD4A gene by comparing the experimentalnresults. Our probabilistic model provides possible scenarios for assembling RNAPII molecules into transcriptionnfactories, where RNAPII and related proteins cooperatively transcribe DNA.