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Review
. 2018 Jan 25;15(1):11.
doi: 10.1186/s12977-018-0393-6.

New windows into retroviral RNA structures

Dhivya Jayaraman  1 , Julia Claire Kenyon  2   3   4
Affiliations
Review

New windows into retroviral RNA structures

Dhivya Jayaraman et al. Retrovirology. .

Abstract

Background: The multiple roles of both viral and cellular RNAs have become increasingly apparent in recent years, and techniques to model them have become significantly more powerful, enabling faster and more accurate visualization of RNA structures.

Main body: Techniques such as SHAPE (selective 2'OH acylation analysed by primer extension) have revolutionized the field, and have been used to examine RNAs belonging to many and diverse retroviruses. Secondary structure probing reagents such as these have been aided by the development of faster methods of analysis either via capillary or next-generation sequencing, allowing the analysis of entire genomes, and of retroviral RNA structures within virions. Techniques to model the three-dimensional structures of these large RNAs have also recently developed.

Conclusions: The flexibility of retroviral RNAs, both structural and functional, is clear from the results of these new experimental techniques. Retroviral RNA structures and structural changes control many stages of the lifecycle, and both the RNA structures themselves and their interactions with ligands are potential new drug targets. In addition, our growing understanding of retroviral RNA structures is aiding our knowledge of cellular RNA form and function.

Keywords: Disruptive technology; HIV; NMR; RNA structure; Retrovirus; SHAPE; Secondary structure.

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Figures

Fig. 1
Fig. 1
The basic principle of RNA structure probing
Fig. 2
Fig. 2
Traditional probing versus high-throughput SHAPE probing. SHAPE reagents streamline and improve the RNA structure probing process. Structure probing reagents are used at limiting dilution, where there is up to one modification per RNA molecule. All potential sites of modification are shown for each reagent. The left hand panel illustrates structure probing with traditional, more specific, reagents, and analysis by gel electrophoresis. The right hand panel shows structure probing with SHAPE reagents and analysis by capillary electrophoresis. It should be noted that it is possible to use either analysis technique for any RNA structure probing reagent
See this image and copyright information in PMC

References

    1. Ehresmann C, Baudin F, Mougel M, Romby P, Ebel JP, Ehresmann B. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987;15(22):9109–9128. doi: 10.1093/nar/15.22.9109. - DOI - PMC - PubMed
    1. Kenyon J, Prestwood L, Lever A. Current perspectives on RNA secondary structure probing. Biochem Soc Trans. 2014;42(4):1251–1255. doi: 10.1042/BST20140084. - DOI - PMC - PubMed
    1. Kenyon JC, Ghazawi A, Cheung WK, Phillip PS, Rizvi TA, Lever AM. The secondary structure of the 5’ end of the FIV genome reveals a long-range interaction between R/U5 and gag sequences, and a large, stable stem-loop. RNA. 2008;14(12):2597–2608. doi: 10.1261/rna.1284908. - DOI - PMC - PubMed
    1. Merino EJ, Wilkinson KA, Coughlan JL, Weeks KM. RNA structure analysis at single nucleotide resolution by selective 2’-hydroxyl acylation and primer extension (SHAPE) J Am Chem Soc. 2005;127(12):4223–4231. doi: 10.1021/ja043822v. - DOI - PubMed
    1. Wilkinson KA, Vasa SM, Deigan KE, Mortimer SA, Giddings MC, Weeks KM. Influence of nucleotide identity on ribose 2’-hydroxyl reactivity in RNA. RNA. 2009;15(7):1314–1321. doi: 10.1261/rna.1536209. - DOI - PMC - PubMed

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