uORF-Tools-Workflow for the determination of translation-regulatory upstream open reading frames.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2019
2019
Historique:
received:
26
04
2019
accepted:
29
08
2019
entrez:
13
9
2019
pubmed:
13
9
2019
medline:
7
3
2020
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 31513641
doi: 10.1371/journal.pone.0222459
pii: PONE-D-19-11867
pmc: PMC6742470
doi:
Substances chimiques
5' Untranslated Regions
0
RNA, Messenger
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0222459Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
J Biol Chem. 2009 Mar 13;284(11):6661-73
pubmed: 19131336
Science. 2009 Apr 10;324(5924):218-23
pubmed: 19213877
Proc Natl Acad Sci U S A. 2009 May 5;106(18):7507-12
pubmed: 19372376
Nature. 2012 May 02;485(7396):109-13
pubmed: 22552098
Cold Spring Harb Perspect Biol. 2012 Oct 01;4(10):null
pubmed: 22815232
Bioinformatics. 2012 Oct 1;28(19):2520-2
pubmed: 22908215
Int J Biochem Cell Biol. 2013 Aug;45(8):1690-700
pubmed: 23624144
EMBO J. 2014 May 2;33(9):981-93
pubmed: 24705786
Wiley Interdiscip Rev RNA. 2014 Nov-Dec;5(6):765-78
pubmed: 24995549
Genome Biol. 2014;15(12):550
pubmed: 25516281
Elife. 2015 Jan 26;4:e03971
pubmed: 25621764
Nat Methods. 2016 Feb;13(2):165-70
pubmed: 26657557
Front Oncol. 2016 May 25;6:128
pubmed: 27252909
Science. 2016 Jun 17;352(6292):1413-6
pubmed: 27313038
J Biol Chem. 2016 Aug 12;291(33):16927-35
pubmed: 27358398
EMBO Rep. 2016 Oct;17(10):1374-1395
pubmed: 27629041
Sci Rep. 2016 Sep 16;6:32886
pubmed: 27633668
Cell Mol Life Sci. 2017 May;74(9):1659-1680
pubmed: 27913822
Nucleic Acids Res. 2018 Jan 4;46(D1):D497-D502
pubmed: 29140531
Nat Commun. 2017 Nov 23;8(1):1749
pubmed: 29170441
Nat Methods. 2018 May;15(5):363-366
pubmed: 29529017
Nucleic Acids Res. 2018 Jun 1;46(10):e61
pubmed: 29538776
Nucleic Acids Res. 2018 Apr 20;46(7):3326-3338
pubmed: 29562350
Nucleic Acids Res. 2018 Oct 12;46(18):e109
pubmed: 29945224
Nat Methods. 2018 Jul;15(7):475-476
pubmed: 29967506
Curr Protoc Mol Biol. 2018 Oct;124(1):e67
pubmed: 30178897
Cell Rep. 2018 Sep 25;24(13):3630-3641.e7
pubmed: 30257221
Cell Rep. 2018 Oct 23;25(4):1097-1108.e5
pubmed: 30355487