While polymerizing a RNA molecule, a RNA polymerase (RNAP) walks step-by-step on the corresponding single-stranded DNA (ssDNA) template in a specific direction. Thus, a RNAP can be regarded as a molecular motor for which the ssDNA template serves as the track. The sites of start and stop of its walk on the DNA mark the two ends of the genetic message that it transcribes into RNA. Interference of transcription of two overlapping genes can strongly influence the levels of their expression, i. e., the overall rate of the synthesis of the corresponding full-length RNA molecules, through suppressive effect of one on the other. Here we model this process as a mixed traffic of two groups of RNAP motors that are characterized by two distinct pairs of on- and off-ramps. Each group polymerizes identical copies of a RNA while the RNAs polymerized by the two groups are different. These models, which may also be viewed as two interfering totally asymmetric simple exclusion processes, account for all modes of transcriptional interference in spite of their extreme simplicity. We study both co-directional and contra-directional traffic of the two groups of RNAP motors. Two special cases of the general model correspond to traffic of bacteriophage RNAP motors and that of non-phage RNAP motors. By a combination of mean-field theory and computer simulation of these models we establish the conditions under which increasing rate of initiation of transcription of one gene can switch off another. However, the mechanisms of switching observed in the traffic of phage-RNAP and non-phage RNAP motors are different. Some of our new predictions can be tested experimentally by correlating the rate of RNA synthesis with the RNAP footprints on the respective DNA templates .
We introduce exclusion models of two distinguishable species of hard rods with their distinct sites of entry and exit under open boundary conditions. In the first model both species of rods move in the same direction whereas in the other two models they move in the opposite direction. These models are motivated by the biological phenomenon known as Transcriptional Interference. Therefore, the rules for the kinetics of the models, particularly the rules for the outcome of the encounter of the rods, are also formulated to mimic those observed in Transcriptional Interference. By a combination of mean-field theory and computer simulation of these models we demonstrate how the flux of one species of rods is completely switched off by the other. Exploring the parameter space of the model we also establish the conditions under which switch-like regulation of two fluxes is possible; from the extensive analysis we discover more than one possible mechanism of this phenomenon .
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While polymerizing a RNA molecule, a RNA polymerase (RNAP) walks step-by-step on the corresponding single-stranded DNA (ssDNA) template in a specific direction. Thus, a RNAP can be regarded as a molecular motor for which the ssDNA template serves as the track. The sites of start and stop of its walk on the DNA mark the two ends of the genetic message that it transcribes into RNA. Interference of transcription of two overlapping genes can strongly influence the levels of their expression, i. e., the overall rate of the synthesis of the corresponding full-length RNA molecules, through suppressive effect of one on the other. Here we model this process as a mixed traffic of two groups of RNAP motors that are characterized by two distinct pairs of on- and off-ramps. Each group polymerizes identical copies of a RNA while the RNAs polymerized by the two groups are different. These models, which may also be viewed as two interfering totally asymmetric simple exclusion processes, account for all modes of transcriptional interference in spite of their extreme simplicity. We study both co-directional and contra-directional traffic of the two groups of RNAP motors. Two special cases of the general model correspond to traffic of bacteriophage RNAP motors and that of non-phage RNAP motors.
We introduce exclusion models of two distinguishable species of hard rods with their distinct sites of entry and exit under open boundary conditions. In the first model both species of rods move in the same direction whereas in the other two models they move in the opposite direction. These models are motivated by the biological phenomenon known as Transcriptional Interference. Therefore, the rules for the kinetics of the models, particularly the rules for the outcome of the encounter of the rods, are also formulated to mimic those observed in Transcriptional Interference.
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establish the conditions under which increasing rate of initiation of transcription of one gene can switch off another. However, the mechanisms of switching observed in the traffic of phage-RNAP and non-phage RNAP motors are different. Some of our new predictions can be tested experimentally by correlating the rate of RNA synthesis with the RNAP footprints on the respective DNA templates
demonstrate how the flux of one species of rods is completely switched off by the other. Exploring the parameter space of the model we also establish the conditions under which switch-like regulation of two fluxes is possible; from the extensive analysis we discover more than one possible mechanism of this phenomenon