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Related Concept Videos

Nonsense-mediated mRNA Decay02:27

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,...
mRNA Stability and Gene Expression02:51

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 Expression02:51

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 Stability01:53

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...
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Related Experiment Video

Updated: Jul 4, 2026

Predicting Gene Silencing Through the Spatiotemporal Control of siRNA Release from Photo-responsive Polymeric Nanocarriers
11:53

Predicting Gene Silencing Through the Spatiotemporal Control of siRNA Release from Photo-responsive Polymeric Nanocarriers

Published on: July 21, 2017

SimChip--computer simulation of mRNA steady states.

Georg Hoffmann1, Rasso Ostermeir, Holger Müller

  • 1Institute for Molecular Oncology, Martinsried, Germany. hoffmann@trillium.de

Clinical Laboratory
|May 31, 2008
PubMed
Summary
This summary is machine-generated.

SimChip is a web tool for in silico gene expression experiments. It models mRNA synthesis and decay to explain gene expression patterns and calculate equilibrium times.

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Related Experiment Videos

Last Updated: Jul 4, 2026

Predicting Gene Silencing Through the Spatiotemporal Control of siRNA Release from Photo-responsive Polymeric Nanocarriers
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Published on: July 21, 2017

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Saccharomyces cerevisiae Metabolic Labeling with 4-thiouracil and the Quantification of Newly Synthesized mRNA As a Proxy for RNA Polymerase II Activity
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Saccharomyces cerevisiae Metabolic Labeling with 4-thiouracil and the Quantification of Newly Synthesized mRNA As a Proxy for RNA Polymerase II Activity

Published on: October 22, 2018

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Gene expression is a fundamental biological process.
  • Understanding gene expression dynamics is crucial for biological research.
  • Current methods for simulating gene expression can be complex.

Purpose of the Study:

  • To develop an accessible computational tool for simulating gene expression.
  • To model mRNA synthesis and decay dynamics.
  • To help researchers understand gene expression patterns and equilibrium.

Main Methods:

  • Developed SimChip, a public Internet program for in silico experiments.
  • Utilized differential equations to model linear mRNA synthesis and non-linear decay.
  • Calculated steady-state concentrations as ratios of synthesis (S) and decay (D) rate constants (c = S/D).

Main Results:

  • SimChip simulates gene upregulation and downregulation.
  • The model explains right-skewed distribution patterns observed in gene expression levels.
  • Calculates the time to reach theoretical equilibrium in gene expression.

Conclusions:

  • SimChip provides a valuable platform for virtual gene expression experiments.
  • The tool aids in understanding the complex dynamics of gene regulation.
  • Facilitates the study of mRNA kinetics and steady-state concentrations.