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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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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.
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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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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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RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
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Analysis of Ribosome Profiling Data.

Carine Legrand1, Khanh Dao Duc2, Francesca Tuorto3,4

  • 1Independent Researcher, Mannheim, Germany.

Methods in Molecular Biology (Clifton, N.J.)
|February 16, 2022
PubMed
Summary
This summary is machine-generated.

We developed RiboVIEW, an R package for quality control and analysis of ribosome profiling data. It enables fast, reliable visualization of ribosome positions and unbiased estimation of translation speed under various conditions.

Keywords:
Bioinformatic analysisRibo-SeqRiboVIEWRibosome profilingTASEP

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genetics

Background:

  • Ribosome profiling (RP) is a powerful technique for studying translational dynamics using high-throughput sequencing.
  • Analysis of RP data requires robust bioinformatic and statistical tools to interpret complex translational changes.

Purpose of the Study:

  • To present a novel methodology for quality control, visualization, and unbiased estimation of translation speed from RP data.
  • To introduce the R package RiboVIEW, designed for efficient analysis of RP datasets.

Main Methods:

  • Development of quality control metrics for ribosome-protected mRNA footprints.
  • Implementation of visualization tools for ribosome positioning within transcripts.
  • Application of a biophysical model to calculate quantitative estimates of local and global translation speed.

Main Results:

  • RiboVIEW provides fast and reliable quality control for ribosome profiling data.
  • The package enables efficient visualization of ribosome positions across different genetic and environmental conditions.
  • Unbiased estimation of translation speed is achieved using quantitative biophysical modeling.

Conclusions:

  • The RiboVIEW package offers a comprehensive solution for analyzing ribosome profiling data.
  • This methodology facilitates the study of translational regulation under diverse conditions, including stress.
  • Accurate assessment of translation speed is crucial for understanding gene expression regulation.