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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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Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
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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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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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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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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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Improved computational analysis of ribosome dynamics from 5'P degradome data using fivepseq.

Lilit Nersisyan1, Maria Ropat1, Vicent Pelechano1

  • 1SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna 171 65, Sweden.

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|February 12, 2021
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Summary

fivepseq is a new tool for analyzing 5' monophosphorylated (5'P) degradome data, revealing insights into RNA decay and ribosome dynamics. It helps identify codon-specific ribosome pauses and frameshifts in yeast and plants.

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Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling
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Area of Science:

  • Molecular Biology
  • Computational Biology
  • Genomics

Background:

  • The 5'-3' co-translational degradation machinery in eukaryotes leaves a footprint of the last translating ribosome.
  • 5' monophosphorylated (5'P) degradome sequencing provides insights into both RNA decay and ribosome dynamics.
  • Existing experimental methods lack reproducible computational tools for analyzing 5'P degradome data.

Purpose of the Study:

  • To introduce fivepseq, an application for the analysis and visualization of 5'P degradome data.
  • To enable reproducible, gene-specific, and metagene analysis of ribosome dynamics and RNA decay.
  • To investigate codon-specific ribosome pauses and their biological implications.

Main Methods:

  • Development and application of the fivepseq computational tool for analyzing 5'P degradome sequencing data.
  • Metagene and gene-specific analysis of ribosome footprints and degradation patterns.
  • Investigation of ribosome pauses in *Saccharomyces cerevisiae* following eIF5A depletion and in *Arabidopsis thaliana*.

Main Results:

  • fivepseq facilitates analysis of ribosome dynamics and RNA decay.
  • Identified codon-specific ribosome pauses and strain-specific degradation frameshifts in yeast.
  • Discovered motif-specific ribosome protection during development and increased ribosome protection at termination in aged *Arabidopsis thaliana*.

Conclusions:

  • fivepseq enhances the biological information derived from 5'P degradome datasets.
  • The tool facilitates reproducible analysis of ribosome dynamics and RNA decay.
  • Improved analysis tools significantly advance the study of gene expression regulation and RNA metabolism.