We introduce an ASEP-like model to describe the effects of RNA polymerase (RNAP) traffic on DNAreplication . It contains two particle species representing RNAP and replication forks (replisomes) , respectively, that can interact leading e. g. to the detachment of RNAPs. An interesting aspect is that the RNAP motion is performed on a lattice that is effectively decreasing in length. Using Monte Carlo simulation and an heuristic analytical approach based on exact results for the ASEP we make predictions for the RNAP traffic that might be tested in future experiments .
We introduce a two-species exclusion model to describe the key features of the conflict between the RNA polymerase (RNAP) motor traffic, engaged in the transcription of a segment of DNA, concomitant with the progress of two DNA replication forks on the same DNA segment. One of the species of particles (P) represents RNAP motors while the other (R) represents replication forks. Motivated by the biological phenomena that this model is intended to capture, a maximum of only two R particles are allowed to enter the lattice from two opposite ends whereas the unrestricted number of P particles constitute a totally asymmetric simple exclusion process (TASEP) in a segment in the middle of the lattice. Consequently, the lattice consists of three segments; the encounters of the P particles with the R particles are confined within the middle segment (segment 2) whereas only the R particles can occupy the sites in the segments 1 and 3. The model captures three distinct pathways for resolving the co-directional as well as head-collision between the P and R particles . Using Monte Carlo simulations and heuristic analytical arguments that combine exact results for the TASEP with mean-field approximations, we predict the possible outcomes of the conflict between the traffic of RNAP motors (P particles engaged in transcription) and the replication forks (R particles). The outcomes, of course, depend on the dynamical phase of the TASEP of P particles. In principle, the model can be adapted to the experimental conditions to account for the data quantitatively .
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an ASEP-like
a two-species exclusion
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effects of
key features of the conflict between the
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traffic on DNAreplication
motor traffic, engaged in the transcription of a segment of DNA, concomitant with the progress of two DNA replication forks on the same DNA segment. One of the species of particles (P) represents RNAP motors while the other (R) represents replication forks. Motivated by the biological phenomena that this model is intended to capture, a maximum of only two R particles are allowed to enter the lattice from two opposite ends whereas the unrestricted number of P particles constitute a totally asymmetric simple exclusion process (TASEP) in a segment in the middle of the lattice. Consequently, the lattice consists of three segments; the encounters of the P particles with the R particles are confined within the middle segment (segment 2) whereas only the R particles can occupy the sites in the segments 1 and 3. The model captures three distinct pathways for resolving the co-directional as well as head-collision between the P and R particles
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It contains two particle species representing RNAP and replication forks (replisomes) , respectively, that can interact leading e. g. to the detachment of RNAPs. An interesting aspect is that the RNAP motion is performed on a lattice that is effectively decreasing in length.
R
simulation and an heuristic analytical approach based on
simulations and heuristic analytical arguments that combine
R
ASEP we make predictions for the RNAP traffic that might be tested in future experiments
TASEP with mean-field approximations, we predict the possible outcomes of the conflict between the traffic of RNAP motors (P particles engaged in transcription) and the replication forks (R particles). The outcomes, of course, depend on the dynamical phase of the TASEP of P particles. In principle, the model can be adapted to the experimental conditions to account for the data quantitatively