Ribosome profiling: new views of translation, from single codons to genome scale

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Abstract

Genome-wide analyses of gene expression have so far focused on the abundance of mRNA species as measured either by microarray or, more recently, by RNA sequencing. However, neither approach provides information on protein synthesis, which is the true end point of gene expression. Ribosome profiling is an emerging technique that uses deep sequencing to monitor in vivo translation. Studies using ribosome profiling have already provided new insights into the identity and the amount of proteins that are produced by cells, as well as detailed views into the mechanism of protein synthesis itself.

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Figure 1: Ribosome footprint profiling.
Figure 2: Analysis of ribosome occupancy data.
Figure 3: Alternative reading frames.
Figure 4: Ribosomal pausing and co-translational processes.
Figure 5: Deconvolving transcription and translation.

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Acknowledgements

The author thanks N. McGlincy and his laboratory members more generally for comments on the manuscript, as well as L. Lareau for her suggestions and for sharing unpublished results. This work was partly supported by the Searle Scholars Program.

Author information

Correspondence to Nicholas T. Ingolia.

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Competing interests

N.T.I. is Inventor on patent application covering ribosome profiling.

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Glossary

Codon usage biases

Enrichment for certain synonymous codons, particularly in well-expressed genes.

Polysome

Several translating ribosomes that are held together by a single mRNA transcript.

Polysome profiling

The analysis of polysomal mRNAs that are fractionated by the number of ribosomes on each transcript.

Reading frame

The sequence within an mRNA that begins at a start codon and that extends to the next in-frame stop codon.

Wobble pairing

Non-Watson–Crick base pairing that permits a single tRNA anti-codon to recognize multiple codons.

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Ingolia, N. Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet 15, 205–213 (2014) doi:10.1038/nrg3645

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