TwisTranscripT: stochastic simulation of the transcription-supercoiling coupling
Bilal El Houdaigui1, Sam Meyer1
1Laboratoire de Microbiologie, Adaptation et Pathogénie, CNRS UMR5240, Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, 69621 Villeurbanne, France.
Bioinformatics (Oxford, England)
|April 2, 2020
Summary
This study introduces TwisTranscripT, the first software to simulate the complex coupling between transcription and DNA supercoiling in bacteria. It offers insights into transcriptional regulation and genome evolution.
Area of Science:
- Molecular Biology
- Genomics
- Computational Biology
Background:
- Transcription and DNA supercoiling exhibit a complex, non-linear coupling.
- This interaction arises from the fundamental relationship between DNA and RNA polymerase.
- The co-regulation of adjacent operons is a conserved phenomenon lacking a clear mechanistic explanation.
Purpose of the Study:
- To present the first software tool for simulating the coupling between transcription and DNA supercoiling.
- To enable quantification of this coupling's contribution to global transcriptional regulation.
- To provide a mechanistic basis for observed co-regulation of adjacent operons.
Main Methods:
- Development of novel simulation software named TwisTranscripT.
- Application of the software to a diverse range of bacterial organisms.
- Utilizing Python 3 for implementation, ensuring cross-platform compatibility.
Main Results:
- TwisTranscripT successfully simulates the dynamic coupling between transcription and DNA supercoiling.
- The software allows for the quantification of supercoiling's role in transcriptional regulation.
- The simulation provides a mechanistic explanation for the co-regulation of adjacent operons.
Conclusions:
- The developed software offers a new tool for studying gene regulation in bacteria.
- Understanding transcription-supercoiling coupling is crucial for comprehending genome evolution.
- TwisTranscripT facilitates research into conserved regulatory mechanisms across bacterial species.
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