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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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Eukaryotic Polyribosome Profile Analysis
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Evaluating data integrity in ribosome footprinting datasets through modelled polysome profiles.

Fabio Hedayioglu1, Emma J Mead2, Patrick B F O'Connor3

  • 1Kent Fungal Group, School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury CT2 7NJ, UK.

Nucleic Acids Research
|August 18, 2022
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Summary

This study introduces a method to reconstruct polysome profiles from ribosome footprinting (Ribo-Seq) data. This approach validates both Ribo-Seq and polysome profiling, aiding in the assessment of Ribo-Seq dataset quality.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • Studying protein synthesis regulation requires assessing transcriptome-wide ribosome binding to mRNAs.
  • Polysome profiling and ribosome footprinting (Ribo-Seq) are key methods, offering different resolutions.
  • Ribo-Seq provides ribosome densities on individual transcripts when combined with mRNA expression data.

Purpose of the Study:

  • To develop methods for relating the information content of polysome profiling and Ribo-Seq.
  • To reconstruct theoretical polysome profiles from ribosome footprinting data.
  • To establish a tool for validating the quality of Ribo-Seq datasets.

Main Methods:

  • Development of computational methods to reconstruct polysome profiles from Ribo-Seq data.
  • Comparison of reconstructed polysome profiles with experimental polysome profiling data.
  • Analysis of inconsistencies in RNA and Ribo-Seq data to identify non-physiological features.

Main Results:

  • The developed method successfully reconstructs theoretical polysome profiles from Ribo-Seq data.
  • Both polysome profiling and Ribo-Seq are validated as reliable experimental tools.
  • Identification of non-physiological features in some published Ribo-Seq datasets, linked to data inconsistencies.

Conclusions:

  • Reconstructed polysome profiles are valuable for assessing the global quality of Ribo-Seq datasets.
  • The method provides a simple, visual approach for dataset quality assessment.
  • This approach is useful for validating new Ribo-Seq datasets during early analysis stages.