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Related Concept Videos

Structure of a Gene01:30

Structure of a Gene

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A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
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Combinatorial Gene Control02:33

Combinatorial Gene Control

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Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
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Regulation of Expression at Multiple Steps01:23

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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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Regulation of Expression Occurs at Multiple Steps02:24

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Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
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Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
Topologically Associated Domains (TADs)
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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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Related Experiment Video

Updated: Oct 20, 2025

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

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Geometry of gene regulatory dynamics.

David A Rand1, Archishman Raju2,3, Meritxell Sáez1,4

  • 1Zeeman Institute for Systems Biology and Infectious Epidemiology Research, University of Warwick, Coventry CV4 7AL, United Kingdom.

Proceedings of the National Academy of Sciences of the United States of America
|September 14, 2021
PubMed
Summary

This study uses geometric methods to represent gene networks as landscapes, revealing how cellular decisions arise from parameter changes. These insights offer intuitive models for embryonic development and spatial pattern formation.

Keywords:
Morse–SmaleTuring modelWaddington landscapebifurcationgene network

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Area of Science:

  • Developmental biology
  • Mathematical biology
  • Systems biology

Background:

  • Embryonic development involves ordered cell differentiation driven by gene networks.
  • Waddington's landscape metaphor visualizes cell fate decisions as flows through valleys.
  • Previous work represented gene networks as potential gradients, supporting Waddington's metaphor.

Purpose of the Study:

  • Extend geometric landscape representations to include parameter dependence.
  • Enumerate all possible three-way cellular decisions based on parameter tuning.
  • Unify and represent various spatial pattern formation models in a potential framework.

Main Methods:

  • Applying geometric methods to gene network models.
  • Representing systems as potential gradients with Riemann metrics.
  • Analyzing parameter dependence and spatial coordinates within the landscape model.

Main Results:

  • Enumerated all three-way cellular decisions realizable by tuning up to two parameters.
  • Expressed standard spatial pattern formation models, including Turing systems, in potential form.
  • Described lateral inhibition as a saddle point and Drosophila eye patterning as bistable potential relaxation.

Conclusions:

  • Geometric reasoning provides intuitive and adaptable dynamic models for embryonic development.
  • The potential landscape framework unifies diverse developmental models.
  • These models are well-suited for fitting time-lapse developmental data.