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Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro?

Global transcriptome investigations often result in the detection of an enormous number of transcripts composed of non-co-linear sequence fragments. Such ‘aberrant’ transcript products may arise from post-transcriptional events or genetic rearrangements, or may otherwise be false positives (sequenci...

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Autores principales: Yu, Chun-Ying, Liu, Hsiao-Jung, Hung, Li-Yuan, Kuo, Hung-Chih, Chuang, Trees-Juen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
RNA
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132752/
https://www.ncbi.nlm.nih.gov/pubmed/25053845
http://dx.doi.org/10.1093/nar/gku643
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author Yu, Chun-Ying
Liu, Hsiao-Jung
Hung, Li-Yuan
Kuo, Hung-Chih
Chuang, Trees-Juen
author_facet Yu, Chun-Ying
Liu, Hsiao-Jung
Hung, Li-Yuan
Kuo, Hung-Chih
Chuang, Trees-Juen
author_sort Yu, Chun-Ying
collection PubMed
description Global transcriptome investigations often result in the detection of an enormous number of transcripts composed of non-co-linear sequence fragments. Such ‘aberrant’ transcript products may arise from post-transcriptional events or genetic rearrangements, or may otherwise be false positives (sequencing/alignment errors or in vitro artifacts). Moreover, post-transcriptionally non-co-linear (‘PtNcl’) transcripts can arise from trans-splicing or back-splicing in cis (to generate so-called ‘circular RNA’). Here, we collected previously-predicted human non-co-linear RNA candidates, and designed a validation procedure integrating in silico filters with multiple experimental validation steps to examine their authenticity. We showed that >50% of the tested candidates were in vitro artifacts, even though some had been previously validated by RT-PCR. After excluding the possibility of genetic rearrangements, we distinguished between trans-spliced and circular RNAs, and confirmed that these two splicing forms can share the same non-co-linear junction. Importantly, the experimentally-confirmed PtNcl RNA events and their corresponding PtNcl splicing types (i.e. trans-splicing, circular RNA, or both sharing the same junction) were all expressed in rhesus macaque, and some were even expressed in mouse. Our study thus describes an essential procedure for confirming PtNcl transcripts, and provides further insight into the evolutionary role of PtNcl RNA events, opening up this important, but understudied, class of post-transcriptional events for comprehensive characterization.
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spelling pubmed-41327522014-12-01 Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro? Yu, Chun-Ying Liu, Hsiao-Jung Hung, Li-Yuan Kuo, Hung-Chih Chuang, Trees-Juen Nucleic Acids Res RNA Global transcriptome investigations often result in the detection of an enormous number of transcripts composed of non-co-linear sequence fragments. Such ‘aberrant’ transcript products may arise from post-transcriptional events or genetic rearrangements, or may otherwise be false positives (sequencing/alignment errors or in vitro artifacts). Moreover, post-transcriptionally non-co-linear (‘PtNcl’) transcripts can arise from trans-splicing or back-splicing in cis (to generate so-called ‘circular RNA’). Here, we collected previously-predicted human non-co-linear RNA candidates, and designed a validation procedure integrating in silico filters with multiple experimental validation steps to examine their authenticity. We showed that >50% of the tested candidates were in vitro artifacts, even though some had been previously validated by RT-PCR. After excluding the possibility of genetic rearrangements, we distinguished between trans-spliced and circular RNAs, and confirmed that these two splicing forms can share the same non-co-linear junction. Importantly, the experimentally-confirmed PtNcl RNA events and their corresponding PtNcl splicing types (i.e. trans-splicing, circular RNA, or both sharing the same junction) were all expressed in rhesus macaque, and some were even expressed in mouse. Our study thus describes an essential procedure for confirming PtNcl transcripts, and provides further insight into the evolutionary role of PtNcl RNA events, opening up this important, but understudied, class of post-transcriptional events for comprehensive characterization. Oxford University Press 2014-08-18 2014-07-22 /pmc/articles/PMC4132752/ /pubmed/25053845 http://dx.doi.org/10.1093/nar/gku643 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle RNA
Yu, Chun-Ying
Liu, Hsiao-Jung
Hung, Li-Yuan
Kuo, Hung-Chih
Chuang, Trees-Juen
Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro?
title Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro?
title_full Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro?
title_fullStr Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro?
title_full_unstemmed Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro?
title_short Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro?
title_sort is an observed non-co-linear rna product spliced in trans, in cis or just in vitro?
topic RNA
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132752/
https://www.ncbi.nlm.nih.gov/pubmed/25053845
http://dx.doi.org/10.1093/nar/gku643
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