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

Dmitry E. Andreev1,2, Viktoriya V. Smirnova1, and Ivan N. Shatsky1,a*

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

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

* To whom correspondence should be addressed.

Received April 30, 2021; Revised June 18, 2021; Accepted June 18, 2021
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.
KEY WORDS: ribosomal profiling, ribosome, translation, protein synthesis, scanning, mRNA, next generation sequencing

DOI: 10.1134/S0006297921090054