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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.
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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Ribosomes01:27

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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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RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
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riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow.

Alexander L Cope1, Felicity Anderson2, John Favate1

  • 1Department of Genetics, Rutgers University, Piscataway, NJ 08854-8082, USA.

Bioinformatics (Oxford, England)
|February 14, 2022
PubMed
Summary

The riboviz 2 package simplifies computational analysis of ribosome profiling (Ribo-seq) data for quantifying protein synthesis. This updated tool offers comprehensive, transcript-centric analysis and visualization, making complex Ribo-seq data more accessible.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Ribosome profiling (Ribo-seq) is a powerful technique for measuring protein synthesis in cells.
  • Analyzing Ribo-seq data is complex and presents challenges due to experimental variations and diverse biological contexts.

Purpose of the Study:

  • To introduce riboviz 2, an enhanced software package for the comprehensive analysis and visualization of Ribo-seq data.
  • To provide a streamlined, end-to-end computational workflow for Ribo-seq data processing.

Main Methods:

  • Development of riboviz 2, an updated riboviz package.
  • Implementation of an analysis workflow using the Nextflow workflow management system.
  • Testing across diverse species and library preparation strategies, including multiplexed samples.

Main Results:

  • riboviz 2 enables comprehensive transcript-centric analysis and visualization of Ribo-seq data.
  • The package offers an end-to-end processing workflow suitable for various organisms and experimental setups.
  • Flexibility is provided through open file formats, facilitating integration of new analytical methods.

Conclusions:

  • riboviz 2 significantly improves the computational analysis of Ribo-seq data.
  • The updated package enhances accessibility and utility for researchers studying protein synthesis.
  • riboviz 2 is a flexible and robust tool for diverse Ribo-seq applications.