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Related Concept Videos

RNA Editing02:23

RNA Editing

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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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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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RNA Stability01:53

RNA Stability

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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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Leaky Scanning02:28

Leaky Scanning

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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Transfer RNA Synthesis02:36

Transfer RNA Synthesis

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One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
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RNA Structure01:23

RNA Structure

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Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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Related Experiment Video

Updated: Mar 3, 2026

DNAzyme-dependent Analysis of rRNA 2’-O-Methylation
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DNAzyme-dependent Analysis of rRNA 2’-O-Methylation

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iRNA-PseU: Identifying RNA pseudouridine sites.

Wei Chen1, Hua Tang2, Jing Ye3

  • 1Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China; Gordon Life Science Institute, Boston, Massachusetts, USA.

Molecular Therapy. Nucleic Acids
|April 22, 2017
PubMed
Summary

Pseudouridine, an abundant RNA modification, is crucial in biology. A new computational tool, iRNA-PseU, accurately predicts pseudouridine sites in RNA sequences, overcoming limitations of experimental methods.

Keywords:
Web-serveriRNA-PseUnucleotide chemical propertynucleotide frequencypseudouridineΨ site

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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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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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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Genomics

Background:

  • Pseudouridine is the most abundant RNA modification, vital for numerous biological processes across various RNA types.
  • Experimental methods for pseudouridine detection are time-consuming and costly, posing challenges in the post-genomic era.
  • Predicting pseudouridine modification sites computationally is essential for advancing RNA research and drug development.

Purpose of the Study:

  • To develop a computational approach for predicting pseudouridine modification sites in RNA sequences.
  • To address the need for efficient and cost-effective methods for identifying pseudouridine sites.
  • To provide a tool that assists researchers in understanding RNA modifications.

Main Methods:

  • Incorporation of nucleotide chemical properties and occurrence frequency density distributions.
  • Utilizing the general form of pseudo nucleotide composition (PseKNC).
  • Development of a predictor named iRNA-PseU.

Main Results:

  • The iRNA-PseU predictor demonstrated superior performance compared to existing methods.
  • Rigorous validation through jackknife tests, independent dataset tests, and genome-wide analysis confirmed its efficacy.
  • A user-friendly web server for iRNA-PseU was established for accessibility to experimental scientists.

Conclusions:

  • iRNA-PseU offers a powerful computational solution for predicting pseudouridine sites in RNA.
  • The tool enhances the efficiency of RNA modification studies and facilitates drug development.
  • The web server democratizes access to advanced RNA modification prediction capabilities.