LABRAT

LABRAT (Lightweight Alignment-Based Reckoning of Alternative Three-prime ends) quantifies alternative polyadenylation (APA) and cleavage site usage from RNAseq data to determine relative APA site usage across experimental conditions.

Key Features:

• Quantification of APA isoforms: Determines the relative abundance of alternative polyadenylation isoforms and APA site usage across samples.
• Integration with transcriptome quantification techniques: Leverages transcriptome quantification methods to produce accurate measurements of APA and cleavage site usage from RNAseq data.
• Classification of APA types: Distinguishes between tandem UTRs and alternative last exons when assessing APA events.

Scientific Applications:

• Subcellular localization studies: Identifies relationships between gene-distal APA and RNA localization across cell types.
• Transcription dynamics: Enables analysis of how transcription speed influences APA site selection.
• Cancer research: Detects transcriptome-wide shifts in APA isoform abundance across hundreds of patient-derived tumor samples and links these shifts with patient prognosis.
• Gene expression correlation: Pinpoints individual genes where APA isoform changes strongly correlate with gene expression.
• RNA-binding protein regulation: Facilitates investigation of the roles of 191 RNA-binding proteins in promoting shifts in APA isoform abundance in vitro and in clinical samples.

Methodology:

Analyzes RNAseq data using transcriptome quantification techniques to quantify APA and cleavage site usage and distinguishes tandem UTRs from alternative last exons during quantification.