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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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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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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.
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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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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.
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pre-mRNA Processing02:01

pre-mRNA Processing

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In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
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What is Gene Expression?01:36

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A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then...
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Analysis of mRNA Nuclear Export Kinetics in Mammalian Cells by Microinjection
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Evaluation of Eukaryotic mRNA Coding Potential.

Alex V Kochetov1,2,3

  • 1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia. ak@bionet.nsc.ru.

Methods in Molecular Biology (Clifton, N.J.)
|October 22, 2024
PubMed
Summary

Eukaryotic messenger RNAs (mRNAs) can encode multiple proteins, but many alternative open reading frames (altORFs) remain unannotated. Simple methods can help map these altORFs, improving genomic and transcriptomic data interpretation.

Keywords:
Gene engineeringTranslationmRNA featuresORF prediction

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Eukaryotic messenger RNAs (mRNAs) are known to encode multiple functional polypeptides.
  • Next-generation sequencing (NGS) and proteomics have identified numerous alternative open reading frames (altORFs).
  • Conventional databases often annotate eukaryotic mRNAs with a single coding sequence (CDS) above a threshold, potentially missing altORFs.

Purpose of the Study:

  • To highlight the significance of unannotated altORFs in understanding gene function.
  • To address the limitations of current annotations in interpreting genomics and transcriptomics data.
  • To introduce simple methods for the preliminary mapping of altORFs.

Main Methods:

  • Review of recent advancements in NGS and proteomics.
  • Analysis of current annotation practices in major nucleotide sequence databases.
  • Exploration of preliminary mapping techniques for altORFs.

Main Results:

  • A vast amount of data on potential altORFs exists but is incomplete.
  • The majority of annotated eukaryotic mRNAs contain only a single CDS.
  • Unannotated altORFs may encode proteins crucial for gene function.
  • Current sequence databanks may limit the interpretation of genomic and transcriptomic data due to missing altORF information.

Conclusions:

  • Accurate prediction of altORFs requires specialized experiments.
  • Simple methods offer a viable approach for preliminary altORF mapping.
  • Improved altORF annotation is essential for comprehensive interpretation of genomic and transcriptomic data.