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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

3.8K
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...
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Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
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Termination of Translation01:44

Termination of Translation

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The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...
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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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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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Updated: Nov 11, 2025

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

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Codon Resolution Analysis of Ribosome Profiling Data.

Alexander Bartholomäus1, Zoya Ignatova2

  • 1GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany.

Methods in Molecular Biology (Clifton, N.J.)
|March 25, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces a user-friendly workflow for ribosome profiling data analysis, making complex translation studies accessible to more scientists. It enables precise analysis of codon-specific translation features without requiring extensive computational expertise.

Keywords:
Analysis pipelineCalibrationCodonDeep sequencingNucleotide resolutionRibo-SeqRibosome profilingTranslation and regulation

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Translation is a fundamental biological process.
  • Ribosome profiling is a powerful technique for global translation analysis.
  • Analyzing ribosome profiling data requires specialized bioinformatics skills, limiting accessibility for many researchers.

Purpose of the Study:

  • To develop an accessible and modifiable workflow for ribosome profiling data analysis.
  • To enable precise determination of codon-specific translation features.
  • To support scientists with limited computational backgrounds in analyzing translation data.

Main Methods:

  • A standardized, command-line based workflow for ribosome profiling data analysis.
  • Precise positioning of ribosome-protected fragments.
  • Step-by-step explanations for ease of use.

Main Results:

  • A comprehensive and user-friendly workflow for ribosome profiling data analysis.
  • Standardized data analysis enabling precise determination of codon-specific translation features.
  • Increased accessibility of advanced translation analysis for experimentalists.

Conclusions:

  • The developed workflow democratizes ribosome profiling data analysis.
  • Scientists without computational expertise can now perform detailed translation studies.
  • Facilitates broader research into codon-specific translation mechanisms.