Modified Method of rRNA Structure Analysis Reveals Novel Characteristics of Box C/D RNA Analogues

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Abstract

Ribosomal RNA (rRNA) maturation is a complex process that involves chemical modifications of the bases or sugar residues of specific nucleotides. One of the most abundant types of rRNA modifications, ribose 2’-O-methylation, is guided by ribonucleoprotein complexes containing small nucleolar box C/D RNAs. Since the majority of 2’-O-methylated nucleotides are located in the most conserved regions of rRNA that comprise functionally important centers of the ribosome, an alteration in a 2’-O-methylation profile can affect ribosome assembly and function. One of the key approaches for localization of 2’-O-methylated nucleotides in long RNAs is a method based on the termination of reverse transcription. The current study presents an adaptation of this method for the use of fluorescently labeled primers and analysis of termination products by capillary gel electrophoresis on an automated genetic analyzer. The developed approach allowed us to analyze the influence of the synthetic analogues of box C/D RNAs on post-transcriptional modifications of human 28S rRNA in MCF-7 cells. It has been established that the transfection of MCF-7 cells with a box C/D RNA analogue leads to an enhanced modification level of certain native sites of 2’-O-methylation in the target rRNA. The observed effect of synthetic RNAs on the 2’-O-methylation of rRNA in human cells demonstrates a path towards targeted regulation of rRNA post-transcriptional maturation. The described approach can be applied in the development of novel diagnostic methods for detecting diseases in humans.

About the authors

Ju. A. Filippova

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University

Author for correspondence.
Email: filippova@niboch.nsc.ru
Россия

G. A. Stepanov

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences

Email: filippova@niboch.nsc.ru
Россия

D. V Semenov

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences

Email: filippova@niboch.nsc.ru
Россия

O. A. Koval

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University

Email: filippova@niboch.nsc.ru
Россия

E. V. Kuligina

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences

Email: filippova@niboch.nsc.ru
Россия

I. V. Rabinov

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences

Email: filippova@niboch.nsc.ru
Россия

V. A. Richter

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences

Email: filippova@niboch.nsc.ru
Россия

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Copyright (c) 2015 Filippova J.A., Stepanov G.A., Semenov D.V., Koval O.A., Kuligina E.V., Rabinov I.V., Richter V.A.

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