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Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
Published on: June 15, 2016
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Non-equilibrium phase transition in a model for supercoiling-dependent DNA transcription
A Bentivoglio1, M Ancona, C A Brackley
1SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK. A.Bentivoglio@sms.ed.ac.uk.
Soft Matter
|April 26, 2018
Summary
This study explores DNA supercoiling's effect on gene transcription. Simulations reveal a potential fluctuation-induced switch between active and silent gene phases, challenging mean-field predictions.
Area of Science:
- Biophysics
- Non-equilibrium statistical mechanics
- Molecular biology
Background:
- DNA supercoiling is crucial for gene regulation.
- Non-equilibrium stochastic models describe complex biological processes.
- Previous models suggest supercoiling influences transcription rates.
Purpose of the Study:
- To investigate a non-equilibrium stochastic model for supercoiling-dependent transcription.
- To analyze the phase transition between active and silent transcriptional states in circular DNA.
- To compare simulation results with mean-field theory predictions.
Main Methods:
- Studied a variant of a non-equilibrium stochastic model.
- Focused on circular DNA with positive supercoiling.
- Employed simulations to analyze the phase transition dynamics.
Main Results:
- Observed a non-equilibrium phase transition between an absorbing (silent) and active (transcribed) phase.
- Simulations suggest a fluctuation-induced discontinuous transition, contrary to mean-field predictions of a continuous transition.
- The magnitude of the transcription rate jump diminishes with an increasing number of genes.
Conclusions:
- The transition between transcribed and silent gene states in this model may be discontinuous and influenced by fluctuations.
- Simulation findings highlight the importance of considering stochastic effects in DNA transcription models.
- The number of genes plays a role in modulating the abruptness of the transcriptional switch.
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