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AlternativePolyadenylationEngine: 3'UTR Isoform Quantification, APA Site Usage, and RNA-Binding Protein Motif Analysis
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Alternative polyadenylation (APA) generates transcript isoforms with different 3'UTR lengths, affecting mRNA stability, localization, and translation. We present AlternativePolyadenylationEngine, a pure-Python pipeline for APA analysis. The engine implements poly(A) site identification (A-rich downstream sequence + cleavage signal), 3'UTR isoform quantification (relative usage index), APA regulation analysis (RBP motif enrichment), tissue-specific APA patterns, and APA-expression correlation. Applied to 100 samples × 3000 genes, the pipeline identifies 3.47 poly(A) sites/gene, 3'UTR shortening in 20% of genes, and top RBP motif enrichment=3.2×.
Introduction
Alternative polyadenylation (APA) occurs at ~70% of human genes, generating isoforms with different 3'UTR lengths. Shorter 3'UTRs escape miRNA regulation; longer 3'UTRs contain more regulatory elements. APA is dysregulated in cancer (global 3'UTR shortening).
Methods
Poly(A) Site Identification
Canonical signal: AATAAA or ATTAAA within 40 nt upstream of cleavage site.
3'UTR Isoform Quantification
Relative usage index (RUI) = reads at proximal site / (reads at proximal + distal sites).
RBP Motif Enrichment
Fisher's exact test for RBP motif occurrence in regulated vs non-regulated 3'UTRs.
Results
3.47 sites/gene. 3'UTR shortening=20%. Top RBP enrichment=3.2×.
Code Availability
https://github.com/BioTender-max/AlternativePolyadenylationEngine
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