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Evolution of the unspliced transcriptome

BACKGROUND: Despite their abundance, unspliced EST data have received little attention as a source of information on non-coding RNAs. Very little is know, therefore, about the genomic distribution of unspliced non-coding transcripts and their relationship with the much better studied regularly splic...

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Autores principales: Engelhardt, Jan, Stadler, Peter F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4546029/
https://www.ncbi.nlm.nih.gov/pubmed/26289325
http://dx.doi.org/10.1186/s12862-015-0437-7
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author Engelhardt, Jan
Stadler, Peter F.
author_facet Engelhardt, Jan
Stadler, Peter F.
author_sort Engelhardt, Jan
collection PubMed
description BACKGROUND: Despite their abundance, unspliced EST data have received little attention as a source of information on non-coding RNAs. Very little is know, therefore, about the genomic distribution of unspliced non-coding transcripts and their relationship with the much better studied regularly spliced products. In particular, their evolution has remained virtually unstudied. RESULTS: We systematically study the evidence on unspliced transcripts available in EST annotation tracks for human and mouse, comprising 104,980 and 66,109 unspliced EST clusters, respectively. Roughly one third of these are located totally inside introns of known genes (TINs) and another third overlaps exonic regions (PINs). Eleven percent are “intergenic”, far away from any annotated gene. Direct evidence for the independent transcription of many PINs and TINs is obtained from CAGE tag and chromatin data. We predict more than 2000 3’UTR-associated RNA candidates for each human and mouse. Fifteen to twenty percent of the unspliced EST cluster are conserved between human and mouse. With the exception of TINs, the sequences of unspliced EST clusters evolve significantly slower than genomic background. Furthermore, like spliced lincRNAs, they show highly tissue-specific expression patterns. CONCLUSIONS: Unspliced long non-coding RNAs are an important, rapidly evolving, component of mammalian transcriptomes. Their analysis is complicated by their preferential association with complex transcribed loci that usually also harbor a plethora of spliced transcripts. Unspliced EST data, although typically disregarded in transcriptome analysis, can be used to gain insights into this rarely investigated transcriptome component. The frequently postulated connection between lack of splicing and nuclear retention and the surprising overlap of chromatin-associated transcripts suggests that this class of transcripts might be involved in chromatin organization and possibly other mechanisms of epigenetic control. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-015-0437-7) contains supplementary material, which is available to authorized users.
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spelling pubmed-45460292015-08-23 Evolution of the unspliced transcriptome Engelhardt, Jan Stadler, Peter F. BMC Evol Biol Research Article BACKGROUND: Despite their abundance, unspliced EST data have received little attention as a source of information on non-coding RNAs. Very little is know, therefore, about the genomic distribution of unspliced non-coding transcripts and their relationship with the much better studied regularly spliced products. In particular, their evolution has remained virtually unstudied. RESULTS: We systematically study the evidence on unspliced transcripts available in EST annotation tracks for human and mouse, comprising 104,980 and 66,109 unspliced EST clusters, respectively. Roughly one third of these are located totally inside introns of known genes (TINs) and another third overlaps exonic regions (PINs). Eleven percent are “intergenic”, far away from any annotated gene. Direct evidence for the independent transcription of many PINs and TINs is obtained from CAGE tag and chromatin data. We predict more than 2000 3’UTR-associated RNA candidates for each human and mouse. Fifteen to twenty percent of the unspliced EST cluster are conserved between human and mouse. With the exception of TINs, the sequences of unspliced EST clusters evolve significantly slower than genomic background. Furthermore, like spliced lincRNAs, they show highly tissue-specific expression patterns. CONCLUSIONS: Unspliced long non-coding RNAs are an important, rapidly evolving, component of mammalian transcriptomes. Their analysis is complicated by their preferential association with complex transcribed loci that usually also harbor a plethora of spliced transcripts. Unspliced EST data, although typically disregarded in transcriptome analysis, can be used to gain insights into this rarely investigated transcriptome component. The frequently postulated connection between lack of splicing and nuclear retention and the surprising overlap of chromatin-associated transcripts suggests that this class of transcripts might be involved in chromatin organization and possibly other mechanisms of epigenetic control. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-015-0437-7) contains supplementary material, which is available to authorized users. BioMed Central 2015-08-20 /pmc/articles/PMC4546029/ /pubmed/26289325 http://dx.doi.org/10.1186/s12862-015-0437-7 Text en © Engelhardt and Stadler. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Engelhardt, Jan
Stadler, Peter F.
Evolution of the unspliced transcriptome
title Evolution of the unspliced transcriptome
title_full Evolution of the unspliced transcriptome
title_fullStr Evolution of the unspliced transcriptome
title_full_unstemmed Evolution of the unspliced transcriptome
title_short Evolution of the unspliced transcriptome
title_sort evolution of the unspliced transcriptome
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4546029/
https://www.ncbi.nlm.nih.gov/pubmed/26289325
http://dx.doi.org/10.1186/s12862-015-0437-7
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