Minimal model of transcriptional elongation processes with pauses
arXiv:1411.4978 · doi:10.1103/PhysRevE.90.050701
Abstract
Fundamental biological processes such as transcription and translation, where a genetic sequence is sequentially read by a macromolecule, have been well described by a classical model of non-equilibrium statistical physics, the totally asymmetric exclusion principle (TASEP). This model describes particles hopping between sites of a one-dimensional lattice, with the particle current determining the transcription or translation rate. An open problem is how to analyze a TASEP where particles can pause randomly, as has been observed during transcription. In this work, we report that surprisingly, a simple mean-field model predicts well the particle current for all values of the average pause duration, using a simple description of blocking behind paused particles.
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- On-site residence time in a driven diffusive system: violation and recovery of mean-field
- Current-density relation in the exclusion process with dynamic obstacles
- Two-species TASEP model: from a simple description to intermittency and travelling traffic jams
- Interference of two co-directional exclusion processes in the presence of a static bottleneck: a biologically motivated model
- A Biologically Motivated Asymmetric Exclusion Process: interplay of congestion in RNA polymerase traffic and slippage of nascent transcript
- A Multispecies Exclusion Model Inspired By Transcriptional Interference
- A biologically motivated three-species exclusion model: effects of leaky scanning and overlapping genes on initiation of protein synthesis