uORF-Tools

uORF-Tools analyzes upstream open reading frames (uORFs) from ribosome profiling (ribo-seq) data to identify and characterize translation-regulatory elements that modulate main ORF translation.

Key Features:

• Workflow Management: Built on the Snakemake workflow management system to automate processing steps and enable reproducible analyses.
• uORF Identification and Annotation: Applies Ribo-TISH to ribo-seq data to identify uORFs and generate uORF annotation files.
• Human uORF Annotation: Provides a precompiled human uORF annotation derived from 35 ribo-seq files.
• RPF-focused Analysis in 5' untranslated region (TLS): Analyzes ribosome protected fragments (RPFs) within 5' untranslated regions (TLS) to locate regulatory elements transcriptome-wide.
• Regulatory Activity Assessment: Quantifies stimulus-induced changes in the ratio of RPFs between main ORFs and associated uORFs to identify candidate translation-inhibitory uORFs.

Scientific Applications:

• Translational regulation studies: Identification and characterization of uORFs to study mechanisms controlling gene expression at the translational level.
• Protein synthesis modulation: Investigation of how uORFs influence main ORF translation and overall protein synthesis.
• Post-transcriptional regulation and stimulus/disease response: Exploration of uORF-mediated regulation in cellular responses to environmental stimuli and disease states.

Methodology:

The workflow uses Snakemake to process ribo-seq data, applies Ribo-TISH to detect and annotate uORFs from ribosome protected fragments (RPFs) within 5' untranslated regions (TLS), and computes ratios of RPFs between main ORFs and associated uORFs, with a provided human uORF annotation compiled from 35 ribo-seq files.