uORF-Tools-Workflow for the determination of translation-regulatory upstream open reading frames.

08:00 EDT 12th September 2019 | BioPortfolio

Summary of "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 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.


Journal Details

This article was published in the following journal.

Name: PloS one
ISSN: 1932-6203
Pages: e0222459


DeepDyve research library

PubMed Articles [13820 Associated PubMed Articles listed on BioPortfolio]

Regulation of human inducible nitric oxide synthase expression by an upstream open reading frame.

The human inducible nitric oxide synthase (iNOS) gene contains an upstream open reading frame (uORF) in its 5'-untranslated region (5'-UTR) implying a translational regulation of iNOS expression. Tran...

SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines.

The complex nature of biological data has driven the development of specialized software tools. Scientific workflow management systems simplify the assembly of such tools into pipelines, assist with j...

IsoProt: A complete and reproducible workflow to analyse iTRAQ/TMT experiments.

Reproducibility has become a major concern in biomedical research. In proteomics, bioinformatic workflows can quickly consist of multiple software tools each with its own set of parameters. Their usag...

G-quadruplex located in the 5'UTR of the BAG-1 mRNA affects both its cap-dependent and cap-independent translation through global secondary structure maintenance.

The anti-apoptotic BAG-1 protein isoforms are known to be overexpressed in colorectal tumors and are considered to be potential therapeutic targets. The isoforms are derived from alternative translati...

Alternative Translation Initiation at a UUG Codon Gives Rise to Two Functional Variants of the Mitochondrial Protein Kgd4.

Kgd4 is a novel subunit of the mitochondrial α-ketoglutarate dehydrogenase complex (KGDH). In yeast, the protein is present in two forms of unknown origin, as there is only one open reading frame and...

Clinical Trials [4362 Associated Clinical Trials listed on BioPortfolio]

Validation of the Questionnaire ASES

Questionnaires are often irreplaceable tools of collection of information in research and in the clinical practice. Coupled with other measures, they can be simple complementary tools, but...

Complete Digital Workflows for the Treatment With Multiple-unit Implant-supported Fixed Dental Prostheses (iFDP)

This study is to assess socio-economic factors, clinical and virtual precision, patient-centered outcomes, and esthetics during the treatment with monolithic multi-unit iFDPs in a complete...

Evaluation of the Accuracy of Full Digital Workflow for Guided Implant Surgery Using the R2 Gate Software

The primary aim of the present study is to compare the accuracy of a full digital workflow for dental implants insertion to a partially digital workflow, for a limited edentulous space (1 ...

Adaptation Process of Patient-Reported Outcomes, an eVALuation Study

Objectives: To identify the respective contributions of back-translations and of the expert committee in the process of cultural adaptation of patient reported outcome with an experimental...

Utilization of Ticagrelor in the Upstream Setting for Non-ST-Segment Elevation Myocardial Infarction (UPSTREAM): An ED-Based Clinical Registry

The primary objective of the UPSTREAM Registry is to address the data gap regarding the course of NSTEMI (Non-ST-Elevation Myocardial Infarction)between ED (Emergency Department) arrival ...

Medical and Biotech [MESH] Definitions

Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.

An interferon regulatory factor that binds upstream TRANSCRIPTIONAL REGULATORY ELEMENTS in the GENES for INTERFERON-ALPHA and INTERFERON-BETA. It functions as a transcriptional activator for the INTERFERON TYPE I genes.

Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.

A multifunctional iron-sulfur protein that is both an iron regulatory protein and cytoplasmic form of aconitate hydratase. It binds to iron regulatory elements found on mRNAs involved in iron metabolism and regulates their translation. Its rate of degradation is increased in the presence of IRON.

A multifunctional iron-sulfur protein that is both an iron regulatory protein and cytoplasmic form of aconitate hydratase. It binds to iron regulatory elements found on mRNAs involved in iron metabolism and regulates their translation. Its RNA binding ability and its aconitate hydrolase activity are dependent upon availability of IRON.

Quick Search

DeepDyve research library

Relevant Topics

Within medicine, nutrition (the study of food and the effect of its components on the body) has many different roles. Appropriate nutrition can help prevent certain diseases, or treat others. In critically ill patients, artificial feeding by tubes need t...

Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...

Searches Linking to this Article