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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

3.6K
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...
3.6K
Improving Translational Accuracy02:07

Improving Translational Accuracy

11.6K
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...
11.6K
Leaky Scanning02:28

Leaky Scanning

5.2K
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...
5.2K
Termination of Translation01:44

Termination of Translation

25.5K
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...
25.5K
Translational Regulation01:29

Translational Regulation

45
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,...
45
Translation01:31

Translation

15.0K
Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes the final step in the expression of genes. This process is carried out by ribosomes, complexes of protein and specialized RNA molecules. Ribosomes, transfer RNA (tRNA), and other proteins produce a chain of amino acids—the polypeptide—as the end product of translation.
Translation Produces the Building Blocks of Life
Proteins are...
15.0K

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Related Experiment Video

Updated: Jul 24, 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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Variational inference for detecting differential translation in ribosome profiling studies.

David C Walker1, Zachary R Lozier2, Ran Bi1

  • 1Department of Statistics, Iowa State University, Ames, IA, United States.

Frontiers in Genetics
|July 10, 2023
PubMed
Summary

We developed riboVI, a new Bayesian model for analyzing ribosome profiling (Ribo-seq) data. It accurately identifies changes in translational efficiency, offering new insights into virus-host interactions.

Keywords:
RNA sequencing (RNA-seq)next-generation sequencingriboVIribosome profiling (Ribo-seq)variational Bayes (VB)variational inference

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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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Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling
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Last Updated: Jul 24, 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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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling
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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Translational efficiency regulates protein synthesis.
  • Ribosome profiling (Ribo-seq) and RNA-sequencing (RNA-seq) measure total and actively translated transcripts.
  • Current Ribo-seq analysis methods have limitations in handling paired experimental designs.

Purpose of the Study:

  • To develop an improved statistical model for Ribo-seq data analysis.
  • To account for the paired nature of Ribo-seq and RNA-seq experiments.
  • To provide a user-friendly software tool for analyzing translational efficiency.

Main Methods:

  • A hierarchical Bayesian generalized linear mixed effects model was proposed.
  • The model incorporates random effects for paired samples.
  • A novel variational Bayesian algorithm was implemented in the "riboVI" software tool.

Main Results:

  • Simulations showed "riboVI" outperforms existing methods in ranking differentially translated genes.
  • "riboVI" effectively controls the false discovery rate.
  • Analysis of real Ribo-seq data revealed novel insights into virus-host interactions, including changes in hormone signaling.

Conclusions:

  • The proposed hierarchical Bayesian model and "riboVI" software offer a superior approach for Ribo-seq data analysis.
  • This method enhances the ability to detect biologically significant changes in translational efficiency.
  • The findings provide new biological insights into virus-host interactions.