Ribosome Profiling: Principles and Variations

Abstract

Ribosome profiling provides a snapshot of ribosome positions and density across the transcriptome at a sub‐codon resolution. By sequencing the entire set of ribosome‐protected mRNA fragments, this powerful approach has been successfully used to measure ribosome dynamics and reveal the hidden coding potential of transcriptome. Since its conceptual inception, ribosome profiling has evolved into a versatile method with many innovative variations. It has been applied to study translation in diverse cell types, adapted to capture specific subsets of ribosomes and further improved to address translational regulation in multicellular organisms. The continuous development of ribosome profiling technologies over the coming decade promises a broad view of translational regulation of gene expression.

Key Concepts

  • Ribosome profiling reveals a global translation snapshot.
  • Ribosome profiling is applicable to diverse cell types.
  • Profiling of specific ribosomes permits analysis of nascent chains.
  • Profiling of initiating ribosomes allows the identification of alternative start codon.
  • Ribosome profiling can be adapted to probe translation in vivo.

Keywords: ribosome profiling; translation; initiation; elongation; genome‐wide; deep‐sequencing

Figure 1. General procedures of ribosome profiling. Translating ribosomes are immobilised on mRNAs before or during cell lysis. Polysome is then converted into monosome by RNase digestion followed by size selection of ribosome‐protected mRNA fragments. cDNA library is constructed using the purified mRNA fragments before sequencing.
Figure 2. Variations of ribosome profiling. Modified ribosome profiling protocol has been developed for different species ranging from bacteria to yeast to mammalian cells. Selective ribosome profiling is designed to capture ribosomes synthesising nascent chains interacting with chaperones or targeting different locations such as ER. Initiating ribosome profiling captures ribosomes stalled at the start codon. Tissue‐specific ribosome profiling permits cell‐type‐specific ribosome profiling in multicellular organisms.
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Further Reading

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Michel AM and Baranov PV (2013) Ribosome profiling: a Hi‐Def monitor for protein synthesis at the genome‐wide scale. Wiley Interdisciplinary Reviews RNA 4: 473–490.

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Wei, Saisai, and Qian, Shu‐Bing(May 2015) Ribosome Profiling: Principles and Variations. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0025984]