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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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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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Improving Translational Accuracy02:07

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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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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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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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Related Experiment Video

Updated: Nov 18, 2025

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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Inferring translational heterogeneity from Saccharomyces cerevisiae ribosome profiling.

Pedro do Couto Bordignon1, Sebastian Pechmann1

  • 1Département de Biochimie, Université de Montréal, Montréal, QC, Canada.

The FEBS Journal
|February 4, 2021
PubMed
Summary

This study reveals programmed translation heterogeneity in yeast, identifying specific 3-codon sequences that are translated at different rates. These differentially translated sequences are linked to cellular homeostasis and protein biosynthesis.

Keywords:
codon biasprotein biogenesisribosome profilingtRNA modificationtranslation regulation

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Ribosome profiling (Ribo-seq) is crucial for studying mRNA translation into proteins.
  • Translation regulation is vital for maintaining cellular homeostasis.
  • Interpreting Ribo-seq data presents challenges, with variability sometimes obscuring biological signals.

Purpose of the Study:

  • To investigate the biological origins of variability in Ribo-seq data.
  • To identify sequence elements that cause programmed translational heterogeneity.
  • To understand how this heterogeneity contributes to cellular functions.

Main Methods:

  • Comparative analysis of Ribo-seq data from Saccharomyces cerevisiae.
  • Systematic identification of short, differentially translated (DT) 3-codon sequences across mRNAs.
  • Linking DT sequences to known translation regulation mechanisms.

Main Results:

  • Variability in Ribo-seq data reflects programmed translational heterogeneity.
  • Identified specific 3-codon sequences with differential translation rates.
  • DT sequences are associated with translation elongation regulation.
  • Enrichment of DT sequences in genes involved in protein and organelle biosynthesis.

Conclusions:

  • Genomic sequences encode translational heterogeneity, optimizing cellular homeostasis.
  • Ribo-seq is a powerful tool for dissecting complex translation regulation.
  • Programmed translational heterogeneity plays a role in cellular function.