Animal-APAdb: a comprehensive animal alternative polyadenylation database

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Alternative polyadenylation (APA) is a key post-transcriptional regulatory mechanism influencing gene expression by generating transcripts with varying 3' untranslated region lengths.
• While APA's role in humans is recognized, comprehensive APA profiles and databases for other animal species are lacking.
• Understanding APA diversity across species is crucial for insights into gene regulation, evolution, and biological processes.

Purpose of the Study:

• To systematically characterize APA profiles across a wide range of animal species.
• To identify and catalog APA events, polyadenylation sites (PAS), and associated motifs in diverse animal taxa.
• To develop a centralized, user-friendly database (Animal-APAdb) for accessing and analyzing animal APA data.

Main Methods:

• Utilized RNA sequencing data from 9,244 public samples across 18 animal species.
• Applied the DaPars2 and QAPA algorithms to identify and quantify APA events.
• Predicted polyadenylation sites (PAS) and analyzed conserved motifs near PAS.

Main Results:

• Identified over 342,952 APA events using DaPars2 and 315,691 APA events using QAPA across the 18 species.
• Cataloged a median of 17,020 to 17,953 APA events per species, revealing significant inter-species variation.
• Developed Animal-APAdb, a comprehensive database featuring extensive APA information, including tissue-specific data.

Conclusions:

• This study provides the first comprehensive characterization of APA profiles in a broad range of animal species.
• The developed Animal-APAdb database serves as a valuable resource for researchers studying animal gene regulation, APA evolution, and related biological mechanisms.
• The findings highlight the importance of APA in diverse animal biology and pave the way for future discoveries in the field.