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Nonsense-mediated mRNA Decay

Nonsense-mediated mRNA Decay

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,...

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

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Nuclear Export of mRNA

Nuclear Export of mRNA

Before mRNAs are exported to the cytoplasm, it is crucial to check each mRNA for structural and functional integrity. Eukaryotic cells use several different mechanisms, collectively known as mRNA surveillance, to look for irregularities in mRNAs. Irregular or aberrant mRNA are rapidly degraded by various enzymes. If a defective mRNA escapes the surveillance, it would be translated into a protein which would either be non-functional or not function properly. One of the primary irregularities in...

Regulation of Expression at Multiple Steps

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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...

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Related Experiment Video

Updated: Mar 3, 2026

Measurement of mRNA Decay Rates in Saccharomyces cerevisiae Using rpb1-1 Strains

Measurement of mRNA Decay Rates in Saccharomyces cerevisiae Using rpb1-1 Strains

Published on: December 13, 2014

Programming mRNA decay to modulate synthetic circuit resource allocation.

Ophelia S Venturelli^1,2, Mika Tei^1,2, Stefan Bauer³

¹California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94158, USA.

Nature Communications

|April 27, 2017

Summary

This summary is machine-generated.

Synthetic biology circuits can be enhanced by degrading host cell transcripts with MazF (sequence-dependent endoribonuclease). Protecting target genes redirects cellular resources, boosting synthetic production and offering a new control strategy.

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Last Updated: Mar 3, 2026

Measurement of mRNA Decay Rates in Saccharomyces cerevisiae Using rpb1-1 Strains

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Published on: December 13, 2014

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

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Determining Genome-wide Transcript Decay Rates in Proliferating and Quiescent Human Fibroblasts

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Published on: January 2, 2018

Area of Science:

Synthetic Biology
Molecular Biology
Systems Biology

Background:

Synthetic circuits in host cells compete for limited intracellular resources.
Global transcriptome degradation can potentially reallocate resources.

Purpose of the Study:

To investigate resource funnelling to synthetic circuits via transcriptome degradation.
To enhance production of target molecules in synthetic biology applications.

Main Methods:

Utilizing sequence-dependent endoribonuclease MazF for global transcriptome degradation.
Recoding target genes to protect them from MazF activity.
Employing proteomics and transcriptional profiling for analysis.
Developing a computational model for feedback loop control.

Main Results:

Significant enhancement in the expression of protected fluorescent reporters.
Increased flux of high-value metabolites in engineered cells.
Identification of a host factor crucial for resource redistribution.
Demonstration of proportional control via a MazF mRNA-decay feedback loop.

Conclusions:

Genome-scale control by MazF-mediated resource allocation enhances synthetic circuit productivity.
Recoding genes is a viable strategy to protect targets from MazF.
Cellular resource allocation is a critical design parameter for synthetic circuits.