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uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames
Ribosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments (RPFs) resides within the protein-coding sequence of mRNAs. However, commonly reads are also found within t...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742470/ https://www.ncbi.nlm.nih.gov/pubmed/31513641 http://dx.doi.org/10.1371/journal.pone.0222459 |
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author | Scholz, Anica Eggenhofer, Florian Gelhausen, Rick Grüning, Björn Zarnack, Kathi Brüne, Bernhard Backofen, Rolf Schmid, Tobias |
author_facet | Scholz, Anica Eggenhofer, Florian Gelhausen, Rick Grüning, Björn Zarnack, Kathi Brüne, Bernhard Backofen, Rolf Schmid, Tobias |
author_sort | Scholz, Anica |
collection | PubMed |
description | Ribosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments (RPFs) resides within the protein-coding sequence of mRNAs. However, commonly reads are also found within the transcript leader sequence (TLS) (aka 5’ untranslated region) preceding the main open reading frame (ORF), indicating the translation of regulatory upstream ORFs (uORFs). Here, we present a workflow for the identification of translation-regulatory uORFs. Specifically, uORF-Tools uses Ribo-TISH to identify uORFs within a given dataset and generates a uORF annotation file. In addition, a comprehensive human uORF annotation file, based on 35 ribo-seq files, is provided, which can serve as an alternative input file for the workflow. To assess the translation-regulatory activity of the uORFs, stimulus-induced changes in the ratio of the RPFs residing in the main ORFs relative to those found in the associated uORFs are determined. The resulting output file allows for the easy identification of candidate uORFs, which have translation-inhibitory effects on their associated main ORFs. uORF-Tools is available as a free and open Snakemake workflow at https://github.com/Biochemistry1-FFM/uORF-Tools. It is easily installed and all necessary tools are provided in a version-controlled manner, which also ensures lasting usability. uORF-Tools is designed for intuitive use and requires only limited computing times and resources. |
format | Online Article Text |
id | pubmed-6742470 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-67424702019-09-20 uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames Scholz, Anica Eggenhofer, Florian Gelhausen, Rick Grüning, Björn Zarnack, Kathi Brüne, Bernhard Backofen, Rolf Schmid, Tobias PLoS One Research Article Ribosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments (RPFs) resides within the protein-coding sequence of mRNAs. However, commonly reads are also found within the transcript leader sequence (TLS) (aka 5’ untranslated region) preceding the main open reading frame (ORF), indicating the translation of regulatory upstream ORFs (uORFs). Here, we present a workflow for the identification of translation-regulatory uORFs. Specifically, uORF-Tools uses Ribo-TISH to identify uORFs within a given dataset and generates a uORF annotation file. In addition, a comprehensive human uORF annotation file, based on 35 ribo-seq files, is provided, which can serve as an alternative input file for the workflow. To assess the translation-regulatory activity of the uORFs, stimulus-induced changes in the ratio of the RPFs residing in the main ORFs relative to those found in the associated uORFs are determined. The resulting output file allows for the easy identification of candidate uORFs, which have translation-inhibitory effects on their associated main ORFs. uORF-Tools is available as a free and open Snakemake workflow at https://github.com/Biochemistry1-FFM/uORF-Tools. It is easily installed and all necessary tools are provided in a version-controlled manner, which also ensures lasting usability. uORF-Tools is designed for intuitive use and requires only limited computing times and resources. Public Library of Science 2019-09-12 /pmc/articles/PMC6742470/ /pubmed/31513641 http://dx.doi.org/10.1371/journal.pone.0222459 Text en © 2019 Scholz et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Scholz, Anica Eggenhofer, Florian Gelhausen, Rick Grüning, Björn Zarnack, Kathi Brüne, Bernhard Backofen, Rolf Schmid, Tobias uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames |
title | uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames |
title_full | uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames |
title_fullStr | uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames |
title_full_unstemmed | uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames |
title_short | uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames |
title_sort | uorf-tools—workflow for the determination of translation-regulatory upstream open reading frames |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742470/ https://www.ncbi.nlm.nih.gov/pubmed/31513641 http://dx.doi.org/10.1371/journal.pone.0222459 |
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