A Biologically Motivated Asymmetric Exclusion Process: interplay of congestion in RNA polymerase traffic and slippage of nascent transcript
arXiv:1810.11661 · doi:10.1103/PhysRevE.99.052122
Abstract
We develope a theoretical framework, based on exclusion process, that is motivated by a biological phenomenon called transcript slippage (TS). In this model a discrete lattice represents a DNA strand while each of the particles that hop on it unidirectionally, from site to site, represents a RNA polymerase (RNAP). While walking like a molecular motor along a DNA track in a step-by-step manner, a RNAP simultaneously synthesizes a RNA chain; in each forward step it elongates the nascent RNA molecule by one unit, using the DNA track also as the template. At some special "slippery" position on the DNA, which we represent as a defect on the lattice, a RNAP can lose its grip on the nascent RNA and the latter's consequent slippage results in a final product that is either longer or shorter than the corresponding DNA template. We develope an exclusion model for RNAP traffic where the kinetics of the system at the defect site captures key features of TS events. We demonstrate the interplay of the crowding of RNAPs and TS. A RNAP has to wait at the defect site for longer period in a more congested RNAP traffic, thereby increasing the likelihood of its suffering a larger number of TS events. The qualitative trends of some of our results for a simple special case of our model are consistent with experimental observations. The general theoretical framework presented here will be useful for guiding future experimental queries and for analysis of the experimental data with more detailed versions of the same model.
arXiv comment14 pages, including 13 Figures
References in corpus (26)
- Statistical Physics of Vehicular Traffic and Some Related Systems
- Nonequilibrium Steady States of Matrix Product Form: A Solver's Guide
- Nonequilibrium Statistical Mechanics of the Zero-Range Process and Related Models
- Non-equilibrium statistical mechanics: From a paradigmatic model to biological transport
- Physics of Transport and Traffic Phenomena in Biology: from molecular motors and cells to organisms
- Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist's perspective
- Stochasticity and traffic jams in the transcription of ribosomal RNA: Intriguing role of termination and antitermination
- Exact Results for the Asymmetric Simple Exclusion Process with a Blockage
- Driven Lattice Gases with Quenched Disorder: Exact Results and Different Macroscopic Regimes
- The Exclusion Process: A paradigm for non-equilibrium behaviour
- Intracellular transport driven by cytoskeletal motors: General mechanisms and defects
- Steady State and Dynamics of Driven Diffusive Systems with Quenched Disorder
- Disordered asymmetric simple exclusion process: mean-field treatment
- Interacting RNA polymerase motors on DNA track: effects of traffic congestion and intrinsic noise on RNA synthesis
- Driven Diffusive Systems with Disorder
- Phase diagram and edge effects in the ASEP with bottlenecks
- Partially Asymmetric Exclusion Processes with Sitewise Disorder
- Single-Bottleneck Approximation for Driven Lattice Gases with Disorder and Open Boundary Conditions
- Asymmetric Exclusion Processes with Disorder: Effect of Correlations
- Defect-induced phase transition in the asymmetric simple exclusion process
- Minimal model of transcriptional elongation processes with pauses
- Collective dynamics of an inhomogeneous two-channel exclusion process: Theory and Monte Carlo simulations
- Entrainment and unit velocity: Surprises in an accelerated exclusion process
- Template-directed biopolymerization: tape-copying Turing machines
- Interference of two co-directional exclusion processes in the presence of a static bottleneck: a biologically motivated model
- RNA polymerase interactions and elongation rate