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REVIEW: Modern Approaches for Identification of Modified Nucleotides in RNA

J. A. Filippova1, D. V. Semenov1, E. S. Juravlev1,2, A. B. Komissarov3,4, V. A. Richter1, and G. A. Stepanov1,2*

1Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; E-mail: stepanovga@niboch.nsc.ru

2Novosibirsk State University, 630090 Novosibirsk, Russia

3Research Institute of Influenza, 197376 St. Petersburg, Russia

4St. Petersburg University, 199034 St. Petersburg, Russia

* To whom correspondence should be addressed.

Received February 28, 2017; Revision received July 17, 2017
This review considers approaches for detection of modified monomers in the RNA structure of living organisms. Recently, some data on dynamic alterations in the pool of modifications of the key RNA species that depend on external factors affecting the cells and physiological conditions of the whole organism have been accumulated. The recent studies have presented experimental data on relationship between the mechanisms of formation of modified/minor nucleotides of RNA in mammalian cells and the development of various pathologies. The development of novel methods for detection of chemical modifications of RNA nucleotides in the cells of living organisms and accumulation of knowledge on the contribution of modified monomers to metabolism and functioning of individual RNA species establish the basis for creation of novel diagnostic and therapeutic approaches. This review includes a short description of routine methods for determination of modified nucleotides in RNA and considers in detail modern approaches that enable not only detection but also quantitative assessment of the modification level of various nucleotides in individual RNA species.
KEY WORDS: post-transcriptional RNA modifications, chemical modifications of nucleotides, minor nucleotides, RNA editing, reverse transcription, mass spectrometry, transcriptome-wide high-throughput sequencing

DOI: 10.1134/S0006297917110013