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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

RNA Stability

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...

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.
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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...

Riboswitches

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...

Nonsense-mediated mRNA Decay

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

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Related Experiment Video

Updated: May 14, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

mRNAStab--a web application for mRNA stability analysis.

Andrei Alic¹, José E Pérez-Ortín, Joaquín Moreno

¹Department of Informatics and Department of Biochemistry and Molecular Biology, Universitat de València, 46100 Burjassot, Spain.

Bioinformatics (Oxford, England)

|January 29, 2013

Summary

This summary is machine-generated.

This study introduces improved algorithms for analyzing mRNA stability using dynamic genomic run-on (GRO) experiments. The software enhances the measurement of transcription and degradation rates for thousands of mRNAs during cellular responses.

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A Reporter Assay to Analyze Intronic microRNA Maturation in Mammalian Cells

A Reporter Assay to Analyze Intronic microRNA Maturation in Mammalian Cells

Published on: June 16, 2022

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Last Updated: May 14, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

A Reporter Assay to Analyze Intronic microRNA Maturation in Mammalian Cells

A Reporter Assay to Analyze Intronic microRNA Maturation in Mammalian Cells

Published on: June 16, 2022

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Eukaryotic gene expression is controlled by transcription and mRNA degradation.
Functional genomics enables simultaneous measurement of transcription (TR) and degradation (DR) rates for numerous mRNAs.
Genomic run-on (GRO) is a key method for assessing mRNA stability and dynamics.

Purpose of the Study:

To present a software package with enhanced algorithms for determining mRNA stability.
To improve the analysis of dynamic genomic run-on (GRO) experiments.
To facilitate the simultaneous measurement of TR and DR rates for thousands of mRNAs.

Main Methods:

Development of novel algorithms for mRNA stability analysis.
Application of the software package to dynamic genomic run-on (GRO) data.
Simultaneous quantification of transcription rates (TR) and degradation rates (DR).

Main Results:

The software provides improved accuracy in determining mRNA stability.
Enhanced algorithms facilitate precise measurement of TR and DR during dynamic cellular responses.
The package supports high-throughput analysis of thousands of mRNA molecules.

Conclusions:

The developed software significantly advances the analysis of mRNA dynamics.
Improved algorithms enhance the understanding of gene expression regulation.
This tool is valuable for functional genomics research involving dynamic mRNA turnover.