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Related Concept Videos

Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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 dimers that...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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 dimers that...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Combinatorial Gene Control02:33

Combinatorial Gene Control

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.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

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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Related Experiment Video

Updated: Jun 19, 2026

An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
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Combinatorial binding predicts spatio-temporal cis-regulatory activity.

Robert P Zinzen1, Charles Girardot, Julien Gagneur

  • 1European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.

Nature
|November 6, 2009
PubMed
Summary
This summary is machine-generated.

Scientists developed a new method to predict gene expression patterns using transcription factor binding data. This approach accurately decodes the regulatory landscape during development without prior knowledge of factor function.

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Related Experiment Videos

Last Updated: Jun 19, 2026

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12:54

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

Area of Science:

  • Developmental Biology
  • Genomics
  • Computational Biology

Background:

  • Precise gene expression patterns are crucial for development, controlled by transcription factors binding to cis-regulatory modules.
  • Genome-wide transcription factor occupancy data is available, but decoding the regulatory landscape remains challenging.

Purpose of the Study:

  • To develop a novel, data-driven approach for predicting spatio-temporal cis-regulatory activity.
  • To create a high-resolution atlas of cis-regulatory modules during Drosophila mesoderm development.

Main Methods:

  • Utilized in vivo transcription factor binding and enhancer activity data.
  • Trained support vector machines using binding profiles of known cis-regulatory modules to predict expression patterns.
  • Employed in vivo transgenic reporter assays to validate predictions.

Main Results:

  • Generated a detailed atlas of cis-regulatory modules and their temporal occupancy.
  • Successfully predicted five spatio-temporal expression patterns with high accuracy.
  • Observed unexpected plasticity in transcription factor binding leading to similar expression outcomes.

Conclusions:

  • The novel approach accurately predicts cis-regulatory activity from transcription factor binding data.
  • This method is widely applicable as it does not require prior knowledge of transcription factor sequence affinity, function, or expression.
  • The findings reveal plasticity in transcription factor binding during development.