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DoGFinder: a software for the discovery and quantification of readthrough transcripts from RNA-seq

BACKGROUND: Recent studies have described a widespread induction of transcriptional readthrough as a consequence of various stress conditions in mammalian cells. This novel phenomenon, initially identified from analysis of RNA-seq data, suggests intriguing new levels of gene expression regulation. H...

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Autores principales: Wiesel, Yuval, Sabath, Niv, Shalgi, Reut
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6083495/
https://www.ncbi.nlm.nih.gov/pubmed/30089468
http://dx.doi.org/10.1186/s12864-018-4983-4
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author Wiesel, Yuval
Sabath, Niv
Shalgi, Reut
author_facet Wiesel, Yuval
Sabath, Niv
Shalgi, Reut
author_sort Wiesel, Yuval
collection PubMed
description BACKGROUND: Recent studies have described a widespread induction of transcriptional readthrough as a consequence of various stress conditions in mammalian cells. This novel phenomenon, initially identified from analysis of RNA-seq data, suggests intriguing new levels of gene expression regulation. However, the mechanism underlying naturally occurring transcriptional readthrough, as well as its regulatory consequences, still remain elusive. Furthermore, the readthrough response to stress has thus far not been investigated outside of mammalian species, and the occurrence of readthrough in many physiological and disease conditions remains to be explored. RESULTS: To facilitate a wider investigation into transcriptional readthrough, we created the DoGFinder software package, for the streamlined identification and quantification of readthrough transcripts, also known as DoGs (Downstream of Gene-containing transcripts), from any RNA-seq dataset. Using DoGFinder, we explore the dependence of DoG discovery potential on RNA-seq library depth, and show that stress-induced readthrough induction discovery is robust to sequencing depth, and input parameter settings. We further demonstrate the use of the DoGFinder software package on a new publically available RNA-seq dataset, and discover DoG induction in human PME cells following hypoxia – a previously unknown readthrough inducing stress type. CONCLUSIONS: DoGFinder will enable users to explore, in a few simple steps, the readthrough phenomenon in any condition and organism. DoGFinder is freely available at https://github.com/shalgilab/DoGFinder. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4983-4) contains supplementary material, which is available to authorized users.
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spelling pubmed-60834952018-08-10 DoGFinder: a software for the discovery and quantification of readthrough transcripts from RNA-seq Wiesel, Yuval Sabath, Niv Shalgi, Reut BMC Genomics Software BACKGROUND: Recent studies have described a widespread induction of transcriptional readthrough as a consequence of various stress conditions in mammalian cells. This novel phenomenon, initially identified from analysis of RNA-seq data, suggests intriguing new levels of gene expression regulation. However, the mechanism underlying naturally occurring transcriptional readthrough, as well as its regulatory consequences, still remain elusive. Furthermore, the readthrough response to stress has thus far not been investigated outside of mammalian species, and the occurrence of readthrough in many physiological and disease conditions remains to be explored. RESULTS: To facilitate a wider investigation into transcriptional readthrough, we created the DoGFinder software package, for the streamlined identification and quantification of readthrough transcripts, also known as DoGs (Downstream of Gene-containing transcripts), from any RNA-seq dataset. Using DoGFinder, we explore the dependence of DoG discovery potential on RNA-seq library depth, and show that stress-induced readthrough induction discovery is robust to sequencing depth, and input parameter settings. We further demonstrate the use of the DoGFinder software package on a new publically available RNA-seq dataset, and discover DoG induction in human PME cells following hypoxia – a previously unknown readthrough inducing stress type. CONCLUSIONS: DoGFinder will enable users to explore, in a few simple steps, the readthrough phenomenon in any condition and organism. DoGFinder is freely available at https://github.com/shalgilab/DoGFinder. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4983-4) contains supplementary material, which is available to authorized users. BioMed Central 2018-08-08 /pmc/articles/PMC6083495/ /pubmed/30089468 http://dx.doi.org/10.1186/s12864-018-4983-4 Text en © The Author(s). 2018 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 Software
Wiesel, Yuval
Sabath, Niv
Shalgi, Reut
DoGFinder: a software for the discovery and quantification of readthrough transcripts from RNA-seq
title DoGFinder: a software for the discovery and quantification of readthrough transcripts from RNA-seq
title_full DoGFinder: a software for the discovery and quantification of readthrough transcripts from RNA-seq
title_fullStr DoGFinder: a software for the discovery and quantification of readthrough transcripts from RNA-seq
title_full_unstemmed DoGFinder: a software for the discovery and quantification of readthrough transcripts from RNA-seq
title_short DoGFinder: a software for the discovery and quantification of readthrough transcripts from RNA-seq
title_sort dogfinder: a software for the discovery and quantification of readthrough transcripts from rna-seq
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6083495/
https://www.ncbi.nlm.nih.gov/pubmed/30089468
http://dx.doi.org/10.1186/s12864-018-4983-4
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