Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Experimental RNAi02:15

Experimental RNAi

6.0K
RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
6.0K
RNA Editing02:23

RNA Editing

8.8K
RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
8.8K
RNA Interference01:23

RNA Interference

25.7K
RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
25.7K
Ribosome Profiling02:24

Ribosome Profiling

3.4K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.4K
RNA-seq03:21

RNA-seq

9.7K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.7K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Extracellular Small RNAs in Human Milk: Molecular Profiles, Stability and Fragment-Specific Responses in Cell-Based Assays.

Non-coding RNA·2026
Same author

The DRAGON benchmark for clinical NLP.

NPJ digital medicine·2025
Same author

Novel transferrin gene mutations in four new cases of congenital Atransferrinaemia: Functional and diagnostic pathogenicity despite negative bioinformatics.

British journal of haematology·2024
Same author

Principles of miRNA/miRNA* function in plant MIRNA processing.

Nucleic acids research·2024
Same author

Iron accumulation drives fibrosis, senescence and the senescence-associated secretory phenotype.

Nature metabolism·2023
Same author

The plant noncoding transcriptome: a versatile environmental sensor.

The EMBO journal·2023
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

Related Experiment Video

Updated: May 9, 2025

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

53.5K

SIREs 3.0, an improved RNA prediction tool for iron-responsive elements.

Clara Suárez-Quintana1,2, Mar Navarro-Padilla3, Uciel Chorostecki2

  • 1Department of Biomedicine, Iron metabolism: Regulation and Diseases Group, Universitat Internacional de Catalunya (UIC), Sant Cugat del Vallès 08195, Spain.

Nucleic Acids Research
|May 5, 2025
PubMed
Summary
This summary is machine-generated.

SIREs 3.0 is an improved web server for identifying iron-responsive elements (IREs) in RNA sequences. This tool aids in understanding iron metabolism regulation and associated human diseases.

More Related Videos

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs
08:49

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

Published on: September 16, 2019

7.5K
Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation
09:07

Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation

Published on: June 21, 2016

8.1K

Related Experiment Videos

Last Updated: May 9, 2025

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

53.5K
Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs
08:49

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

Published on: September 16, 2019

7.5K
Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation
09:07

Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation

Published on: June 21, 2016

8.1K

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genetics

Background:

  • Iron-responsive elements (IREs) are crucial RNA motifs regulating iron metabolism genes via iron regulatory proteins (IRPs).
  • Dysregulation of the IRP/IRE system is implicated in various human diseases.
  • The SIREs web server facilitates the identification of IREs in nucleotide sequences.

Purpose of the Study:

  • To present SIREs 3.0, an upgraded web server for predicting IREs.
  • To enhance the prediction accuracy and user experience for IRE analysis.
  • To provide researchers with advanced tools for studying iron metabolism regulation.

Main Methods:

  • Developed a Flask-based framework for improved interconnectivity.
  • Integrated NCBI and Ensembl APIs for fetching genomic data.
  • Introduced novel input modes (batch, transcript, gene) and updated IRE motifs based on in vivo data.

Main Results:

  • SIREs 3.0 offers improved IRE prediction by incorporating transcript location and novel motifs.
  • Enhanced scoring system and graphical representations improve data interpretation.
  • The web server now features a more responsive and accessible interface across devices.

Conclusions:

  • SIREs 3.0 provides a powerful and versatile platform for IRE prediction.
  • The enhanced features facilitate large-scale and single-gene analyses of iron metabolism.
  • This tool supports research into diseases linked to IRP/IRE system disruptions.