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Related Concept Videos

Nuclear Export of mRNA02:31

Nuclear Export of mRNA

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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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RNA Stability01:53

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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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Regulation of Expression at Multiple Steps01:23

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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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Nonsense-mediated mRNA Decay02:27

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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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A Method for Measuring RNA N6-methyladenosine Modifications in Cells and Tissues
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New Twists in Detecting mRNA Modification Dynamics.

Ina Anreiter1, Quoseena Mir2, Jared T Simpson1

  • 1Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada.

Trends in Biotechnology
|July 5, 2020
PubMed
Summary
This summary is machine-generated.

Modified nucleotides in messenger RNA (mRNA) are crucial for gene expression. New single-molecule sequencing technologies offer promising solutions to analyze these modifications, despite bioinformatic challenges.

Keywords:
2′-O-ribose methylationNanoporem(5)Cm(6)Am(6)AmmRNA modifications

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2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications
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2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

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Area of Science:

  • Epitranscriptomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Modified nucleotides extend the standard genetic code in animals, plants, and viruses.
  • Epitranscriptomics studies mRNA modifications and their effects on gene expression.
  • Low abundance and technical hurdles limit systematic analysis of these modifications.

Purpose of the Study:

  • To review the progress and bioinformatic challenges of using single-molecule sequencing for analyzing mRNA modifications.
  • To highlight the potential of Oxford Nanopore sequencing in epitranscriptomics.

Main Methods:

  • Review of current literature on epitranscriptomics and single-molecule sequencing.
  • Focus on bioinformatic approaches for analyzing modified nucleotide data from Oxford Nanopore sequencing.

Main Results:

  • Selective chemical and immunological methods have provided candidate topology maps of mRNA modifications.
  • Single-molecule sequencing, particularly Oxford Nanopore, presents a promising technological advance.
  • Significant bioinformatic challenges remain in analyzing the data generated by this novel sequencing technology.

Conclusions:

  • Overcoming bioinformatic challenges is essential for advancing epitranscriptomics.
  • Single-molecule sequencing holds significant potential for detailed analysis of mRNA modifications.
  • Further technical advancements are needed to increase confidence in mapping nucleotide modifications.