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Related Concept Videos

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...
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...
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

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...
Transcriptional Regulation: Riboswitches01:23

Transcriptional Regulation: Riboswitches

Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
Riboswitches01:56

Riboswitches

Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...

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Related Experiment Video

Updated: Jun 20, 2026

Electrophoretic Mobility Shift Assay (EMSA) for the Study of RNA-Protein Interactions: The IRE/IRP Example
12:44

Electrophoretic Mobility Shift Assay (EMSA) for the Study of RNA-Protein Interactions: The IRE/IRP Example

Published on: December 3, 2014

Direct Fe2+ sensing by iron-responsive messenger RNA:repressor complexes weakens binding.

Mateen A Khan1, William E Walden, Dixie J Goss

  • 1Department of Chemistry, Hunter College, City University of New York, New York, New York 10065, USA.

The Journal of Biological Chemistry
|September 2, 2009
PubMed
Summary

Iron (Fe2+) directly weakens the binding of regulatory proteins to iron-responsive element (IRE) RNAs. This finding reveals a new mechanism for iron regulation of gene expression, complementing known pathways.

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Electrophoretic Mobility Shift Assay (EMSA) for the Study of RNA-Protein Interactions: The IRE/IRP Example
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Published on: April 25, 2018

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Iron Metabolism

Background:

  • Iron is essential for cellular function but tightly regulated.
  • Iron regulation involves interactions between iron-responsive element (IRE) RNAs and iron-regulatory proteins (IRPs).
  • Existing models focus on protein modification and degradation for iron-induced mRNA translation control.

Purpose of the Study:

  • To investigate the direct role of Fe(2+) in the binding affinity between IRE-RNAs and IRPs.
  • To elucidate the impact of metal ions on IRE-RNA:IRP complex stability.
  • To compare the effects of Fe(2+) on different IRE-RNA structures.

Main Methods:

  • Studied Fe(2+) binding to ferritin and mitochondrial aconitase IRE-RNA:repressor complexes in the absence of O(2).
  • Measured changes in K(d) values to quantify binding affinity.
  • Utilized Mn(2+) as an O(2)-resistant surrogate for Fe(2+) to assess metal ion binding to IRE-RNA and IRP fluorescence.

Main Results:

  • Fe(2+) significantly weakens IRE-RNA:IRP binding, increasing K(d) by 17-fold.
  • Fe(2+) decreases the stability of ferritin IRE-RNA:IRP complexes 5-10 times more than mitochondrial aconitase IRE-RNA:IRP complexes.
  • Metal ions bind to IRE-RNA, not IRPs, affecting RNA structure.

Conclusions:

  • Fe(2+) directly modulates IRE-RNA:IRP interactions, adding a novel layer to iron regulation.
  • Differential responses to Fe(2+) are influenced by specific IRE-RNA structural variations.
  • This direct iron interaction provides a complementary mechanism to existing iron regulatory pathways.