APA-Scan

APA-Scan detects alternative polyadenylation (APA) events in 3'-untranslated regions (3'-UTRs) by integrating RNA-seq and 3'-end-seq data to identify and evaluate polyadenylation sites across biological conditions.

Key Features:

• High-Resolution Analysis: Leverages predicted and experimentally validated polyadenylation signals as references to increase resolution of 3'-UTR APA site detection beyond read-coverage-only approaches.
• Three-Step Workflow: Computes read coverage across 3'-UTR regions, identifies potential APA sites and assesses their significance between two biological conditions, and produces graphical representations that integrate 3'-UTR annotations with read coverage data.
• Integration with RNA-seq and 3'-end-seq: Integrates RNA-seq and 3'-end-seq data to provide comprehensive detection and high-resolution short-read coverage plots for transcriptome-wide 3'-UTR APA events.
• Validation and Performance: Tested on simulated and real RNA-seq datasets and validated with 3'-end-seq and qPCR in mouse embryonic fibroblast cells, demonstrating superior accuracy relative to DaPars and APAtrap.
• Implementation: Implemented in Python 3 and compatible with Windows, Linux, and Mac platforms.

Scientific Applications:

• Post-transcriptional regulation analysis: Identifies 3'-UTR length variations to study effects on mRNA stability and translation efficiency.
• microRNA and RNA-binding protein interaction studies: Enables investigation of how APA-mediated 3'-UTR changes alter microRNA and RNA-binding protein interactions.
• Discovery of unannotated APA events: Detects unannotated 3'-UTR APA events across conditions to expand transcript annotation.

Methodology:

Computes read coverage across 3'-UTRs, uses predicted and experimentally validated polyadenylation signals to identify potential APA sites, assesses significance between two biological conditions, integrates RNA-seq and 3'-end-seq data, and generates high-resolution coverage plots.