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 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.
Metadaten
Author:Anica Scholz, Florian Eggenhofer, Rick Gelhausen, Björn Grüning, Katharina ZarnackORCiDGND, Bernhard BrüneORCiD, Rolf Backofen, Tobias SchmidORCiD
URN:urn:nbn:de:hebis:30:3-510788
DOI:https://doi.org/10.1371/journal.pone.0222459
ISSN:1932-6203
Pubmed Id:https://pubmed.ncbi.nlm.nih.gov/31513641
Parent Title (English):PLoS one
Publisher:PLoS
Place of publication:Lawrence, Kan.
Contributor(s):Eric Jan
Document Type:Article
Language:English
Year of Completion:2019
Date of first Publication:2019/09/12
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2019/09/16
Tag:5' UTR; Cellular stress responses; Gene prediction; Genome annotation; Messenger RNA; Protein translation; Ribosomes; Translation initiation
Volume:14
Issue:(9): e0222459
Page Number:9
First Page:1
Last Page:9
Note:
Copyright: © 2019 Scholz et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
HeBIS-PPN:454157002
Institutes:Medizin / Medizin
Exzellenzcluster / Exzellenzcluster Makromolekulare Komplexe
Wissenschaftliche Zentren und koordinierte Programme / Sonderforschungsbereiche / Forschungskollegs
Dewey Decimal Classification:6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 610 Medizin und Gesundheit
Sammlungen:Universitätspublikationen
Open-Access-Publikationsfonds:Medizin
Licence (German):License LogoCreative Commons - Namensnennung 4.0