Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

RNA-seq

RNA-seq

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 microarray-based...

Ribosome Profiling

Ribosome Profiling

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 helps...

mRNA Stability and Gene Expression

mRNA Stability and Gene Expression

The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity.
Cis-acting Elements involved in mRNA stability

mRNA Stability and Gene Expression

mRNA Stability and Gene Expression

The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity.
Cis-acting Elements involved in mRNA stability

You might also read

Related Articles

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

Sort by

Same author

Peroxisomal Degradation Correlates with the Progression of Kidney Injury in a UUO Mouse Model.

Biology·2026

Same author

Effects of Dietary Choline Supplementation on Production Performance and Liver Characteristics in Late-Laying Hens.

Animals : an open access journal from MDPI·2026

Same author

Incidence and Prognostic Implications of Mental Disorders Among Patients With a Permanent Pacemaker: A Nationwide Cohort Study.

Journal of the American Heart Association·2026

Same author

Defining the Therapeutic Ceiling of Endovascular Thrombectomy in Large-Core Stroke: Beyond the Limits of ASPECTS.

Stroke·2026

Same author

The Risks of Mortality, Cardiovascular Events, and Pulmonary Complications in Cancer Patients Who Smoke Cigarettes and Switch to E-Cigarettes: South Korea, 2015‒2022.

American journal of public health·2026

Same author

Peroxisome Carrier SLC25A17: Potential Biomarker for Peroxisome Dysfunction and Human Disease.

International journal of molecular sciences·2026

Search research articles

Related Experiment Video

Updated: May 30, 2026

Using the E1A Minigene Tool to Study mRNA Splicing Changes

Using the E1A Minigene Tool to Study mRNA Splicing Changes

Published on: April 22, 2021

IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data.

Hyunsoo Kim¹, Yingtao Bi, Sharmistha Pal

¹Center for Systems and Computational Biology, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104-4268, USA.

BMC Bioinformatics

|July 29, 2011

Summary

We developed IsoformEx, a novel algorithm for accurate transcript isoform quantification from mRNA sequencing (mRNA-Seq) data. This method improves gene expression analysis by effectively handling complex exon structures.

More Related Videos

Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA

Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA

Published on: October 27, 2011

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

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

Published on: March 7, 2018

Related Experiment Videos

Last Updated: May 30, 2026

Using the E1A Minigene Tool to Study mRNA Splicing Changes

Using the E1A Minigene Tool to Study mRNA Splicing Changes

Published on: April 22, 2021

Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA

Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA

Published on: October 27, 2011

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

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:

Bioinformatics
Computational Biology
Genomics

Background:

Messenger RNA sequencing (mRNA-Seq) is a powerful transcriptomics tool for gene and isoform identification.
Accurate quantification of transcript isoform expression from mRNA-Seq data remains challenging due to factors like constitutive exons.

Purpose of the Study:

To introduce a novel algorithm, IsoformEx, for precise estimation of transcript isoform expression levels.
To address the challenges in isoform quantification posed by complex exon structures in mRNA-Seq data.

Main Methods:

Developed IsoformEx, an algorithm utilizing weighted non-negative least squares estimation.
Validated the algorithm using in silico mRNA-Seq simulations and real mRNA-Seq data with qRT-PCR experiments.

Main Results:

IsoformEx demonstrated accurate estimation of transcript expression levels in simulations and real data.
The algorithm showed higher correlation with known expression levels in simulated data compared to existing methods.
IsoformEx exhibited superior agreement with qRT-PCR measurements for specific transcripts in real mRNA-Seq data.

Conclusions:

IsoformEx provides a fast and accurate method for estimating both transcript and gene expression levels.
The algorithm effectively accounts for short and alternative exons through a weighting scheme.
The IsoformEx software is publicly available for research use.