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Conserved Secondary Structures in Viral mRNAs

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...

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Autores principales: Kiening, Michael, Ochsenreiter, Roman, Hellinger, Hans-Jörg, Rattei, Thomas, Hofacker, Ivo, Frishman, Dmitrij
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563262/
https://www.ncbi.nlm.nih.gov/pubmed/31035717
http://dx.doi.org/10.3390/v11050401
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author Kiening, Michael
Ochsenreiter, Roman
Hellinger, Hans-Jörg
Rattei, Thomas
Hofacker, Ivo
Frishman, Dmitrij
author_facet Kiening, Michael
Ochsenreiter, Roman
Hellinger, Hans-Jörg
Rattei, Thomas
Hofacker, Ivo
Frishman, Dmitrij
author_sort Kiening, Michael
collection PubMed
description 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).
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spelling pubmed-65632622019-06-17 Conserved Secondary Structures in Viral mRNAs Kiening, Michael Ochsenreiter, Roman Hellinger, Hans-Jörg Rattei, Thomas Hofacker, Ivo Frishman, Dmitrij Viruses Article 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). MDPI 2019-04-29 /pmc/articles/PMC6563262/ /pubmed/31035717 http://dx.doi.org/10.3390/v11050401 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Kiening, Michael
Ochsenreiter, Roman
Hellinger, Hans-Jörg
Rattei, Thomas
Hofacker, Ivo
Frishman, Dmitrij
Conserved Secondary Structures in Viral mRNAs
title Conserved Secondary Structures in Viral mRNAs
title_full Conserved Secondary Structures in Viral mRNAs
title_fullStr Conserved Secondary Structures in Viral mRNAs
title_full_unstemmed Conserved Secondary Structures in Viral mRNAs
title_short Conserved Secondary Structures in Viral mRNAs
title_sort conserved secondary structures in viral mrnas
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563262/
https://www.ncbi.nlm.nih.gov/pubmed/31035717
http://dx.doi.org/10.3390/v11050401
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