TY  - JOUR
A1  - Scholz, Anica
A1  - Eggenhofer, Florian
A1  - Gelhausen, Rick
A1  - Grüning, Björn
A1  - Zarnack, Katharina
A1  - Brüne, Bernhard
A1  - Backofen, Rolf
A1  - Schmid, Tobias
T1  - uORF-tools—workflow for the determination of translation-regulatory upstream open reading frames
T2  - PLoS one
N2  - 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.
KW  - Protein translation
KW  - Ribosomes
KW  - Gene prediction
KW  - Translation initiation
KW  - Cellular stress responses
KW  - Genome annotation
KW  - Messenger RNA
KW  - 5' UTR
Y1  - 2019
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/51078
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-510788
SN  - 1932-6203
N1  - 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.
VL  - 14
IS  - (9): e0222459
SP  - 1
EP  - 9
PB  - PLoS
CY  - Lawrence, Kan.
ER  -