TwisTranscripT

TwisTranscripT simulates the coupling between transcription and DNA supercoiling in bacteria to study how this interaction modulates gene expression and operon co-regulation.

Key Features:

• Simulation of Transcription-Supercoiling Coupling (TSC): Models interactions between DNA and RNA polymerase and captures the non-linear dynamics of supercoiling during transcription.
• Quantification of Global Transcriptional Regulation: Quantifies the impact of TSC on global genome-wide gene expression patterns.
• Mechanistic Basis for Co-regulation of Operons: Provides mechanistic modeling to explain co-regulation of adjacent operons in bacterial genomes.

Scientific Applications:

• Gene Expression Studies: Dissects regulatory networks controlling gene expression in response to environmental changes via TSC simulation.
• Genome Evolution Research: Investigates evolutionary conservation and adaptation of operon co-regulation in bacterial genomes.

Methodology:

Implemented in Python3 and leveraging the Python scientific computing ecosystem; supports adaptation of topoisomerase parameters, although such adaptations have not been empirically tested.