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Conserved Secondary Structures in Viral mRNAs

1
Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany
2
Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währingerstr. 29, 1090 Vienna, Austria
3
Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstrasse 17, 1090 Vienna, Austria
4
Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
5
St. Petersburg State Polytechnic University, St. Petersburg 195251, Russia
*
Author to whom correspondence should be addressed.
Viruses 2019, 11(5), 401; https://doi.org/10.3390/v11050401
Received: 30 March 2019 / Revised: 23 April 2019 / Accepted: 26 April 2019 / Published: 29 April 2019
(This article belongs to the Special Issue Virus Bioinformatics)
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Abstract

RNA secondary structure in untranslated and protein coding regions has been shown to play an important role in regulatory processes and the viral replication cycle. While structures in non-coding regions have been investigated extensively, a thorough overview of the structural repertoire of protein coding mRNAs, especially for viruses, is lacking. Secondary structure prediction of large molecules, such as long mRNAs remains a challenging task, as the contingent of structures a sequence can theoretically fold into grows exponentially with sequence length. We applied a structure prediction pipeline to Viral Orthologous Groups that first identifies the local boundaries of potentially structured regions and subsequently predicts their functional importance. Using this procedure, the orthologous groups were split into structurally homogenous subgroups, which we call subVOGs. This is the first compilation of potentially functional conserved RNA structures in viral coding regions, covering the complete RefSeq viral database. We were able to recover structural elements from previous studies and discovered a variety of novel structured regions. The subVOGs are available through our web resource RNASIV (RNA structure in viruses). View Full-Text
Keywords: mRNA structure; structure database; secondary structure; viral mRNA; subVOG; structurally related; RNA structure; structurally homogenous; structurally related; mRNA families mRNA structure; structure database; secondary structure; viral mRNA; subVOG; structurally related; RNA structure; structurally homogenous; structurally related; mRNA families
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Supplementary materials

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    Link: http://rnasiv.bio.wzw.tum.de/sup/index.html
    Description: The following are available online at http://rnasiv.bio.wzw.tum.de/sup/index.html, Figure S1: virus lineages included in the VOGs, Figure S2: Mean pairwise sequence identity of VOG alignments as a function of VOG size, Figure S3: Sequence Alignment of a protein from Heliothis virescens ascovirus 3e and proteins belonging to the mRNAs of subVOG 64 of VOG00003, Table S1: Clustering of GO terms of subVOG proteins and the average structural coverage of their corresponding mRNAs, Table S2: Clustering of GO terms of subVOG proteins and the average structural coverage of their corresponding mRNAs (regardless of GO evidence codes).
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Kiening, M.; Ochsenreiter, R.; Hellinger, H.-J.; Rattei, T.; Hofacker, I.; Frishman, D. Conserved Secondary Structures in Viral mRNAs. Viruses 2019, 11, 401.

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