movAPA

movAPA analyzes alternative polyadenylation by profiling and quantifying poly(A) sites and 3' UTR modifications from 3' end sequencing and RNA-seq to characterize tissue- and condition-specific APA dynamics.

Key Features:

• Comprehensive Analysis Pipeline: Provides preprocessing, annotation, and statistical analysis functions for poly(A) site datasets.
• Poly(A) Site Profiling: Profiles APA dynamics across biological samples to reveal tissue-specific and condition-specific polyadenylation patterns.
• Identification of Poly(A) Signals: Detects poly(A) signals to support interpretation of regulatory mechanisms underlying APA.
• Metrics for Tissue-Specificity and Usage: Computes seven distinct metrics to quantify tissue-specificity and usage patterns of APA sites across samples.
• Detection of 3' UTR Modifications: Implements three methods to identify 3' UTR shortening and lengthening events between conditions.
• Exploration of APA Site Switching: Enables analysis of APA site switching including non-3' UTR polyadenylation events.
• Scalability and Flexibility: Demonstrated on poly(A) site data from rice and mouse sperm cells and applicable to tissue-level and single-cell contexts.

Scientific Applications:

• Gene expression regulation: Characterizes how alternative polyadenylation alters mRNA isoform abundance and UTR-mediated regulation.
• Developmental biology: Identifies APA changes associated with developmental stage- or tissue-specific programs.
• Cancer research: Detects APA alterations that can affect oncogene or tumor suppressor regulation via 3' UTR remodeling.
• Plant science: Profiles poly(A) site usage and APA dynamics in plant samples such as rice.
• Single-cell transcriptomics: Supports profiling APA dynamics in single-cell contexts to reveal cell-type-specific polyadenylation patterns.

Methodology:

Processes 3' end sequencing and RNA-seq data with preprocessing, annotation, and statistical analysis; identifies poly(A) signals; computes seven tissue-specificity/usage metrics; applies three methods to detect 3' UTR shortening/lengthening; implemented for use within R.