3USS

3USS identifies and characterizes alternative 3' untranslated regions (3'UTRs) of protein-coding genes from RNA-seq data to detect changes in 3'UTR length arising from alternative polyadenylation.

Key Features:

• Automatic Identification: Automatically detects alternative 3'UTRs, reporting both shorter and longer variants relative to a reference transcriptome using RNA-seq data.
• Novelty Detection: Flags 3'UTRs as putative novel when they are absent from available genomic annotations.
• Comparative Analysis: Identifies common and sample-specific alternative 3'UTRs when two related RNA-seq samples are provided.

Scientific Applications:

• Gene Expression Regulation: Relates 3'UTR length variation to effects on mRNA stability, localization, and translation by altering microRNA binding sites and RNA-binding protein motifs.
• Post-transcriptional Modifications: Investigates the role of alternative polyadenylation and 3'UTR changes in mRNA processing and stability.
• Disease Mechanisms: Explores how aberrant 3'UTR usage may contribute to disease pathogenesis, including cancers with dysregulated alternative splicing and polyadenylation.

Methodology:

Maps RNA-seq reads to genomic coordinates, detects regions that deviate from the reference transcriptome indicative of alternative polyadenylation, and annotates and flags putative novel alternative 3'UTRs.