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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,...

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,...

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...

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...

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...

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

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Related Experiment Video

Updated: May 29, 2026

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

A critical role for noncoding 5S rRNA in regulating Mdmx stability.

Muyang Li¹, Wei Gu

¹Institute for Cancer Genetics, College of Physicians and Surgeons, Columbia University, 1130 Saint Nicholas Avenue, New York, NY 10032, USA.

|September 20, 2011

Summary

Noncoding 5S ribosomal RNA (rRNA) inhibits the degradation of Mdmx protein by Mdm2. Knocking down 5S rRNA triggers Mdmx degradation, activating p53-dependent growth arrest in cancer cells.

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Identification of RNA Fragments Resulting from Enzymatic Degradation using MALDI-TOF Mass Spectrometry

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Last Updated: May 29, 2026

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

Identification of RNA Fragments Resulting from Enzymatic Degradation using MALDI-TOF Mass Spectrometry

Identification of RNA Fragments Resulting from Enzymatic Degradation using MALDI-TOF Mass Spectrometry

Published on: April 11, 2022

Area of Science:

Molecular biology
Cancer research
RNA biology

Background:

The p53 tumor suppressor pathway is crucial for preventing cancer.
Mdm2 is a key negative regulator of p53, targeting it for degradation.
Mdmx protein stabilizes p53 but is itself stable in many cancers, posing a therapeutic challenge.

Purpose of the Study:

To elucidate the mechanism regulating Mdmx protein stability.
To investigate the role of noncoding RNA in the p53-Mdmx regulatory axis.
To identify novel therapeutic targets for modulating Mdmx stability in cancer.

Main Methods:

Affinity purification and mass spectrometry to identify Mdmx-associated proteins.
RNA interference (RNAi) to knockdown endogenous 5S rRNA.
Western blotting to assess protein levels and ubiquitination.
Cellular assays to evaluate growth arrest.

Main Results:

5S rRNA was identified as a major component of Mdmx-associated complexes.
5S rRNA directly binds to the RING domain of Mdmx, inhibiting its ubiquitination by Mdm2.
Knockdown of 5S rRNA significantly increased Mdmx degradation and activated p53-dependent growth arrest.
Mdm2-mediated p53 ubiquitination remained unaffected by 5S rRNA levels.

Conclusions:

Noncoding 5S rRNA acts as a natural inhibitor of Mdmx degradation by Mdm2.
5S rRNA plays a critical role in modulating the stability of the Mdmx protein.
Targeting 5S rRNA offers a potential strategy to reactivate the p53 pathway in cancer therapy.