uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames
Autoři:
Anica Scholz aff001; Florian Eggenhofer aff002; Rick Gelhausen aff002; Björn Grüning aff002; Kathi Zarnack aff003; Bernhard Brüne aff001; Rolf Backofen aff002; Tobias Schmid aff001
Působiště autorů:
Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt am Main, Germany
aff001; Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
aff002; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, Frankfurt am Main, Germany
aff003; Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany
aff004
Vyšlo v časopise:
PLoS ONE 14(9)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0222459
Souhrn
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.
Klíčová slova:
Biology and life sciences – Genetics – Gene expression – Protein translation – Translation initiation – Genomics – Genome analysis – Gene prediction – Genome annotation – Transcriptome analysis – Biochemistry – Ribosomes – Nucleic acids – RNA – Messenger RNA – Cell biology – Cellular structures and organelles – Cell processes – Cellular stress responses – Computational biology
Zdroje
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