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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

3.7K
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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Translational Regulation01:29

Translational Regulation

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Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
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Stringent Response in E. coli01:23

Stringent Response in E. coli

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Bacterial growth is closely tied to nutrient availability, with cells proliferating exponentially under favorable conditions and entering a stationary phase when resources become scarce. This transition is mediated by a regulatory mechanism known as the stringent response, which allows bacteria to adapt to nutrient deprivation by modulating gene expression and metabolic activity.During nutrient scarcity, intracellular amino acid levels decline. It results in the accumulation of uncharged tRNAs...
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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

12.0K
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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Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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Related Experiment Video

Updated: Oct 21, 2025

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA
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Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

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Single-cell Ribo-seq reveals cell cycle-dependent translational pausing.

Michael VanInsberghe1, Jeroen van den Berg2, Amanda Andersson-Rolf2

  • 1Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, The Netherlands. m.vaninsberghe@hubrecht.eu.

Nature
|September 9, 2021
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Summary
This summary is machine-generated.

Researchers developed a sensitive single-cell ribosome profiling method. This technique, integrated with machine learning, achieves codon resolution to study translation and cell-to-cell variations.

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RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
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Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling
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Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling

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Related Experiment Videos

Last Updated: Oct 21, 2025

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA
10:15

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

Published on: July 6, 2012

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RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
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Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling
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Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling

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Area of Science:

  • Molecular Biology
  • Genomics
  • Cell Biology

Background:

  • Single-cell sequencing advances genome, epigenome, and transcriptome analysis.
  • Measuring translation at the single-cell level remains a significant challenge.
  • Existing protein detection methods lack single-cell resolution for translation.

Purpose of the Study:

  • To develop a highly sensitive method for ribosome profiling in single cells.
  • To achieve single-codon resolution for analyzing cellular translation.
  • To investigate the role of translation in cellular diversity.

Main Methods:

  • Enhanced ribosome profiling protocols for increased sensitivity.
  • Integration with machine learning for single-codon resolution.
  • Validation in various cellular contexts, including rare cell types.

Main Results:

  • Demonstrated amino acid limitation causing ribosome pausing at specific codons.
  • Observed cell-cycle-dependent ribosome pausing.
  • Detected pronounced GAA codon pausing during mitosis.
  • Applied the technique to rare primary enteroendocrine cells.

Conclusions:

  • The developed technology enables sensitive, high-resolution analysis of single-cell translation.
  • Ribosome pausing is linked to specific cellular states like the cell cycle and mitosis.
  • This method is applicable to rare cell populations, opening new research avenues.
  • Provides a foundational tool for understanding translational contributions to cell diversity.