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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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Ribosomes01:27

Ribosomes

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Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
Ribosome Structure and Assembly
Ribosomes are composed of ribosomal RNA (rRNA) and proteins. In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome...
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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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Translation in Prokaryotes01:29

Translation in Prokaryotes

393
Prokaryote translation is a complex, highly coordinated process that converts genetic information from mRNA into functional proteins. It involves three stages: initiation, elongation, and termination, each facilitated by specific molecular components.Initiation of TranslationThe process begins with the assembly of the ribosomal subunits and initiation factors on the mRNA. In bacteria, the 30S ribosomal subunit recognizes the Shine-Dalgarno sequence in the mRNA, a conserved region upstream of...
393
Termination of Translation01:44

Termination of Translation

26.0K
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...
26.0K
Leaky Scanning02:28

Leaky Scanning

5.3K
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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Related Experiment Video

Updated: Oct 15, 2025

Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale
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Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling.

Alexander L Cope1,2, Sangeevan Vellappan1,3, John S Favate1,2

  • 1Department of Genetics, Rutgers University, Piscataway, NJ, USA.

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

This study presents a refined ribosome profiling protocol for bacteria, yeast, and mammalian cells, alongside the RiboViz tool for data analysis and visualization. These advancements aim to simplify translatome measurements and enhance gene expression insights.

Keywords:
Antibiotic inhibitorsFootprintingRNARibo-seqRibosome profilingTranslation initiation

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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
  • Bioinformatics

Background:

  • Ribosome profiling measures the translatome, offering insights into gene expression regulation.
  • Despite advancements, ribosome profiling data acquisition and analysis remain complex.
  • Previous methods have limitations in standardization and accessibility.

Purpose of the Study:

  • To present an integrated laboratory protocol for ribosome profiling across diverse species.
  • To introduce RiboViz, a computational tool for analyzing and visualizing ribosome profiling data.
  • To improve the accessibility and reproducibility of translatome measurements.

Main Methods:

  • Integration of elements from three established ribosome profiling protocols.
  • Development and application of the RiboViz software for data pre-processing and mapping.
  • Utilization of raw sequencing reads and transcriptome information (FASTA, GFF) as input.

Main Results:

  • A standardized protocol for ribosome profiling in bacteria, yeast, and mammalian cells.
  • RiboViz facilitates efficient analysis and quality control visualization of ribosome profiling data.
  • The combined approach simplifies complex translatome measurements.

Conclusions:

  • The described protocol and RiboViz tool enhance the practical application of ribosome profiling.
  • These resources aid researchers in gaining deeper insights into post-transcriptional gene regulation.
  • The study contributes to more accessible and robust translatome analysis.