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Related Concept Videos

The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Related Experiment Video

Updated: Jun 24, 2026

Humanized Mediator Release Assay as a Read-Out for Allergen Potency
10:22

Humanized Mediator Release Assay as a Read-Out for Allergen Potency

Published on: June 29, 2021

Where does mediator bind in vivo?

Xiaochun Fan1, Kevin Struhl

  • 1Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.

Plos One
|April 4, 2009
PubMed
Summary

Mediator complex association with yeast promoters is selective, not widespread. Our findings clarify Mediator

Area of Science:

  • Molecular Biology
  • Yeast Genetics
  • Gene Regulation

Background:

  • The Mediator complex is crucial for RNA polymerase II transcription, recruited by activators to enhancers.
  • Mediator's role in yeast promoter association is debated, with conflicting reports under different growth conditions.
  • Previous studies suggested widespread Mediator binding in yeast, particularly in synthetic complete (SC) medium.

Purpose of the Study:

  • To resolve the controversy regarding Mediator complex association with yeast promoters.
  • To determine the specific conditions and locations of Mediator binding in Saccharomyces cerevisiae.

Main Methods:

  • Chromatin immunoprecipitation (ChIP) assays to detect Mediator binding.
  • Genome-wide analysis using microarrays to assess Mediator targets.

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Site-Directed Immobilization of Bone Morphogenetic Protein 2 to Solid Surfaces by Click Chemistry
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Humanized Mediator Release Assay as a Read-Out for Allergen Potency
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  • Comparison of Mediator association in YPD and SC media under various conditions.

    • Main Results:

    • Mediator targets are limited in yeast, with few observed in SC medium compared to YPD.
    • Most previously reported genome-wide Mediator targets are false positives due to lenient cut-offs and technical artifacts.
    • Apparent Mediator binding in coding regions is a non-specific accessibility effect, not direct association.

    Conclusions:

    • Mediator complex does not bind broadly across the yeast genome.
    • Mediator selectively associates with a limited set of upstream promoter regions.
    • Mediator binding is dependent on specific activators and environmental stress conditions.