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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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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. |
format | Online Article Text |
id | pubmed-6083495 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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