Homologous SV40 RNA trans-splicing: Special case or prime example of viral RNA trans-splicing?
To date the Simian Virus 40 (SV40) is the only proven example of a virus that recruits the mechanism of RNA trans-splicing to diversify its sequences and gene products. Thereby, two identical viral transcripts are efficiently joined by homologous trans-splicing triggering the formation of a highly t...
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doaj-c330455438244b0995c296dfb586d69f2020-11-25T00:14:05ZengElsevierComputational and Structural Biotechnology Journal2001-03702014-06-011016515710.1016/j.csbj.2014.07.001Homologous SV40 RNA trans-splicing: Special case or prime example of viral RNA trans-splicing?Sushmita Poddar0Joachim Eul1Volker Patzel2Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Block MD4, Level 5, 5 Science Drive 2, Singapore 117597, SingaporeINEIDFO GmbH, Weserstrasse 23, 12045 Berlin, GermanyDepartment of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Block MD4, Level 5, 5 Science Drive 2, Singapore 117597, SingaporeTo date the Simian Virus 40 (SV40) is the only proven example of a virus that recruits the mechanism of RNA trans-splicing to diversify its sequences and gene products. Thereby, two identical viral transcripts are efficiently joined by homologous trans-splicing triggering the formation of a highly transforming 100 kDa super T antigen. Sequences of other viruses including HIV-1 and the human adenovirus type 5 were reported to be involved in heterologous trans-splicing towards cellular or viral sequences but the meaning of these events remains unclear. We computationally and experimentally investigated molecular features associated with viral RNA trans-splicing and identified a common pattern: Viral RNA trans-splicing occurs between strong cryptic or regular viral splice sites and strong regular or cryptic splice sites of the trans-splice partner sequences. The majority of these splice sites are supported by exonic splice enhancers. Splice sites that could compete with the trans-splicing sites for cis-splice reactions are weaker or inexistent. Finally, all but one of the trans-splice reactions seem to be facilitated by one or more complementary binding domains of 11 to 16 nucleotides in length which, however occur with a statistical probability close to one for the given length of the involved sequences. The chimeric RNAs generated via heterologous viral RNA trans-splicing either did not lead to fusion proteins or led to proteins of unknown function. Our data suggest that distinct viral RNAs are highly susceptible to trans-splicing and that heterologous viral trans-splicing, unlike homologous SV40 trans-splicing, represents a chance event.http://www.sciencedirect.com/science/article/pii/S2001037014000105Alternative splicingRNA trans-splicingViral RNA trans-splicingSV40HIV-1Adenovirus |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Sushmita Poddar Joachim Eul Volker Patzel |
spellingShingle |
Sushmita Poddar Joachim Eul Volker Patzel Homologous SV40 RNA trans-splicing: Special case or prime example of viral RNA trans-splicing? Computational and Structural Biotechnology Journal Alternative splicing RNA trans-splicing Viral RNA trans-splicing SV40 HIV-1 Adenovirus |
author_facet |
Sushmita Poddar Joachim Eul Volker Patzel |
author_sort |
Sushmita Poddar |
title |
Homologous SV40 RNA trans-splicing: Special case or prime example of viral RNA trans-splicing? |
title_short |
Homologous SV40 RNA trans-splicing: Special case or prime example of viral RNA trans-splicing? |
title_full |
Homologous SV40 RNA trans-splicing: Special case or prime example of viral RNA trans-splicing? |
title_fullStr |
Homologous SV40 RNA trans-splicing: Special case or prime example of viral RNA trans-splicing? |
title_full_unstemmed |
Homologous SV40 RNA trans-splicing: Special case or prime example of viral RNA trans-splicing? |
title_sort |
homologous sv40 rna trans-splicing: special case or prime example of viral rna trans-splicing? |
publisher |
Elsevier |
series |
Computational and Structural Biotechnology Journal |
issn |
2001-0370 |
publishDate |
2014-06-01 |
description |
To date the Simian Virus 40 (SV40) is the only proven example of a virus that recruits the mechanism of RNA trans-splicing to diversify its sequences and gene products. Thereby, two identical viral transcripts are efficiently joined by homologous trans-splicing triggering the formation of a highly transforming 100 kDa super T antigen. Sequences of other viruses including HIV-1 and the human adenovirus type 5 were reported to be involved in heterologous trans-splicing towards cellular or viral sequences but the meaning of these events remains unclear. We computationally and experimentally investigated molecular features associated with viral RNA trans-splicing and identified a common pattern: Viral RNA trans-splicing occurs between strong cryptic or regular viral splice sites and strong regular or cryptic splice sites of the trans-splice partner sequences. The majority of these splice sites are supported by exonic splice enhancers. Splice sites that could compete with the trans-splicing sites for cis-splice reactions are weaker or inexistent. Finally, all but one of the trans-splice reactions seem to be facilitated by one or more complementary binding domains of 11 to 16 nucleotides in length which, however occur with a statistical probability close to one for the given length of the involved sequences. The chimeric RNAs generated via heterologous viral RNA trans-splicing either did not lead to fusion proteins or led to proteins of unknown function. Our data suggest that distinct viral RNAs are highly susceptible to trans-splicing and that heterologous viral trans-splicing, unlike homologous SV40 trans-splicing, represents a chance event. |
topic |
Alternative splicing RNA trans-splicing Viral RNA trans-splicing SV40 HIV-1 Adenovirus |
url |
http://www.sciencedirect.com/science/article/pii/S2001037014000105 |
work_keys_str_mv |
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