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Related Concept Videos

DNA Topoisomerases02:02

DNA Topoisomerases

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Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types. ...
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Co-activators and Co-repressors02:04

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Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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RNA Polymerase II Accessory Proteins02:36

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Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
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Master Transcription Regulators02:23

Master Transcription Regulators

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Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
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Bacterial Transcription01:53

Bacterial Transcription

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RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
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Related Experiment Video

Updated: Jun 10, 2025

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
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Modeling Control of Supercoiling Dynamics and Transcription Using DNA-Binding Proteins.

Harris Clark, Aleczander Taylor, Enoch Yeung

    IEEE Control Systems Letters
    |October 11, 2024
    PubMed
    Summary

    This study introduces a novel biophysical mechanism for controlling gene transcription by modulating DNA supercoiling. Researchers demonstrate precise control over transcription rates and mRNA levels using mathematical models and simulations.

    Keywords:
    Biological systemsBiomolecular systemsNonlinear control

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    Area of Science:

    • Biophysics
    • Systems Biology
    • Molecular Biology

    Background:

    • Transcription is essential for gene networks and biological circuitry.
    • Controlling transcription is key for synthetic biology and understanding gene regulation.

    Purpose of the Study:

    • To investigate controlling transcription via localized DNA supercoiling.
    • To develop a mathematical model for supercoiling-driven transcription control.

    Main Methods:

    • Developed a reaction network model for transcription and supercoiling dynamics.
    • Formulated a nonlinear state-space model with radial basis function nonlinearity.
    • Utilized control Lyapunov functions for stabilizing control law design.
    • Modeled DNA binding proteins to control supercoiling propagation.

    Main Results:

    • Demonstrated that supercoiling modulation directly controls transcription rates.
    • Showed that mRNA steady-state levels are controllable by adjusting genetic spacing.
    • Illustrated programmable control of transcriptional bursting and pulsatile responses.
    • Established a globally exponentially stable equilibrium point for the system.

    Conclusions:

    • Localized supercoiling offers a new biophysical mechanism for precise transcription control.
    • Mathematical modeling provides a framework for designing synthetic gene circuits with tunable outputs.
    • This approach enables direct control over mRNA levels and dynamic transcriptional patterns.