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Ribosome Profiling02:24

Ribosome Profiling

3.9K
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.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.9K
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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What is Gene Expression?01:36

What is Gene Expression?

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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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Improving Translational Accuracy02:07

Improving Translational Accuracy

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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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Improving Translational Accuracy02:07

Improving Translational Accuracy

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pre-mRNA Processing02:01

pre-mRNA Processing

55.5K
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.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl...
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Related Experiment Video

Updated: Nov 17, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

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IsoTV: processing and visualizing functional features of translated transcript isoforms.

Siddharth Annaldasula1,2, Martyna Gajos1,2, Andreas Mayer1

  • 1Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany.

Bioinformatics (Oxford, England)
|February 15, 2021
PubMed
Summary
This summary is machine-generated.

Researchers can now assess the functional impact of transcript isoforms on proteins using IsoTV. This pipeline analyzes RNA sequencing data to visualize isoform features, aiding in understanding protein diversity.

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Last Updated: Nov 17, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Transcript isoform discovery is accelerating due to advanced RNA sequencing technologies.
  • Functional differences between transcript isoforms from the same gene are often unclear.
  • Understanding isoform variation is crucial for assessing proteome diversity and function.

Purpose of the Study:

  • To develop a computational pipeline for analyzing and visualizing the functional features of translated transcript isoforms.
  • To enable researchers to assess the potential functional consequences of transcript isoform variation on the proteome.
  • To provide a tool for interpreting complex transcriptomic data.

Main Methods:

  • Developed IsoTV, a versatile pipeline for processing and analyzing transcript isoform data.
  • IsoTV integrates gene/isoform expression, transcript composition, and functional features.
  • The pipeline supports various data types, including short- and long-read RNA-seq data from eukaryotic organisms.

Main Results:

  • IsoTV generates easy-to-interpret visualizations of transcript isoform features.
  • Demonstrated IsoTV's utility with Oxford Nanopore long-read data in cancer cell types.
  • Facilitated the understanding of potential protein isoform function and its implications.

Conclusions:

  • IsoTV provides a valuable resource for researchers studying transcript isoform variation.
  • The pipeline enhances the interpretation of functional differences between protein isoforms.
  • IsoTV aids in bridging the gap between transcriptomic data and proteomic function.