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Related Concept Videos

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...
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
Master Transcription Regulators02:23

Master Transcription Regulators

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...
Master Transcription Regulators02:23

Master Transcription Regulators

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...
Eukaryotic Transcription Activators02:42

Eukaryotic Transcription Activators

Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These domains are...

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

Published on: December 3, 2014

SIREs: searching for iron-responsive elements.

Monica Campillos1, Ildefonso Cases, Matthias W Hentze

  • 1European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Nucleic Acids Research
|May 13, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces SIREs, a new web server tool that improves the detection of iron-responsive elements (IREs) in messenger RNA. This enhanced prediction helps in understanding iron metabolism and related human diseases.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genetics

Background:

  • The iron regulatory protein/iron-responsive element (IRP/IRE) system is vital for post-transcriptional gene regulation, controlling iron metabolism.
  • Disruptions in this system are linked to various human diseases.
  • Iron-responsive elements (IREs) are RNA motifs in mRNAs that bind IRPs, regulating protein translation.

Purpose of the Study:

  • To develop an improved computational tool for predicting functional IREs.
  • To address the limitations of existing IRE prediction software, which exhibit insufficient sensitivity.
  • To provide a user-friendly web server for IRE analysis.

Main Methods:

  • Development of the SIREs (Search for iron-responsive elements) web server.
  • Implementation of a simple data input interface for users.
  • Integration of RNA structure analysis, folding predictions, energy data, and a quality flag based on known IRE properties.

Main Results:

  • The SIREs web server offers enhanced sensitivity for detecting functional IREs.
  • It provides comprehensive analysis including structural insights and folding predictions.
  • Results are presented in an easily interpretable tabular and schematic visual format.

Conclusions:

  • The SIREs web server represents a significant advancement in IRE prediction accuracy and usability.
  • This tool aids researchers in studying iron regulation and associated pathologies.
  • The freely accessible web server facilitates broader research in the field of iron metabolism.