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Modifications of Ribosome Profiling that Provide New Data on the Translation Regulation

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Abstract

Ribosome profiling (riboseq) has opened the possibilities for the genome-wide studies of translation in all living organisms. This method is based on deep sequencing of mRNA fragments protected by the ribosomes from hydrolysis by ribonucleases, the so-called ribosomal footprints (RFPs). Ribosomal profiling together with RNA sequencing allows not only to identify with a reasonable accuracy translated reading frames in the transcriptome, but also to track changes in gene expression in response to various stimuli. Notably, ribosomal profiling in its classical version has certain limitations. The size of the selected mRNA fragments is 25-35 nts, while RFPs of other sizes are usually omitted from analysis. Also, ribosomal profiling “averages” the data from all ribosomes and does not allow to study specific ribosomal complexes associated with particular translation factors. However, recently developed modifications of ribosomal profiling provide answers to a number of questions. Thus, it has become possible to analyze not only elongating, but also scanning and reinitiating ribosomes, to study events associated with the collision of ribosomes during mRNA translation, to discover new ways of cotranslational assembly of multisubunit protein complexes during translation, and to selectively isolate ribosomal complexes associated with certain protein factors. New data obtained using these modified approaches provide a better understanding of the mechanisms of translation regulation and the functional roles of translational apparatus components.

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Abbreviations

AMP-PNP:

non-hydrolysable analogue of ATP

eIF:

eukaryotic initiation factor

ORF:

open reading frame

PIC:

preinitiation complex

RFP:

ribosomal footprint

RSC:

ribosomal scanning complex

RQC:

quality control on translating ribosomes

UTR:

untranslated region

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Funding

This work was supported by the Russian Science Foundation (project no. 19-14-00152).

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Authors and Affiliations

  1. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia

    Dmitry E. Andreev, Viktoriya V. Smirnova & Ivan N. Shatsky

  2. Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, Moscow, Russia

    Dmitry E. Andreev

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  1. Dmitry E. Andreev
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  2. Viktoriya V. Smirnova
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  3. Ivan N. Shatsky
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Correspondence to Ivan N. Shatsky.

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The authors declare no conflict of interest in financial or any other sphere. This article does not contain description of studies with the involvement of humans or animal subjects performed by any of the authors.

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Andreev, D.E., Smirnova, V.V. & Shatsky, I.N. Modifications of Ribosome Profiling that Provide New Data on the Translation Regulation. Biochemistry Moscow 86, 1095–1106 (2021). https://doi.org/10.1134/S0006297921090054

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  • DOI: https://doi.org/10.1134/S0006297921090054

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