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Related Concept Videos

Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

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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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Nuclear Export of mRNA02:31

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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...
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RNA Editing02:23

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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mRNA Stability and Gene Expression02:51

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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

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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
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Integrative and accurate annotations enhance current nonsense-mediated mRNA decay rules.

Hiroyuki Iha1,2, Chie Kikutake1, Mikita Suyama1

  • 1Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.

Nucleic Acids Research
|December 1, 2025
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Summary
This summary is machine-generated.

Premature termination codons (PTCs) cause genetic diseases. Improved nonsense-mediated mRNA decay (NMD) rules, considering multi-nucleotide variants and translation, enhance disease impact assessment by 12.0%.

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Area of Science:

  • Genetics
  • Molecular Biology
  • Bioinformatics

Background:

  • Premature termination codons (PTCs) are a significant cause of human genetic diseases.
  • Nonsense-mediated mRNA decay (NMD) is a cellular surveillance pathway that degrades mRNAs with PTCs, preventing truncated protein synthesis.
  • Previous models of NMD efficiency based on PTC position explain only a portion of observed variability.

Purpose of the Study:

  • To enhance the accuracy of NMD escape rules by incorporating additional genetic and transcriptomic factors.
  • To improve the assessment of disease-causing potential for variants generating PTCs.

Main Methods:

  • Utilized matched human genome and transcriptome data from 1086 individuals.
  • Re-evaluated NMD efficiency by integrating multi-nucleotide variants (MNVs), translation status, and RNA isoform expression.
  • Employed accurate annotation strategies for comprehensive data assessment.

Main Results:

  • Achieved a 12.0% improvement in the explanatory power of NMD efficiency through integrated data assessment and accurate annotation.
  • Identified that variants with high allele frequency or low genomic conservation escape NMD.
  • Found that MNVs and lack of ribosomal translation contribute to NMD escape.

Conclusions:

  • Accurate annotation, including MNVs and translation status, is critical for understanding NMD efficiency.
  • The findings provide a more comprehensive framework for assessing the impact of nonsense variants in genetic disease.
  • This improved understanding can aid in diagnosing and managing genetic disorders caused by PTCs.