APA-Scan: Detection and Visualization of 3'-UTR APA with RNA-seq and 3'-end-seq Data

• Published in: bioRxiv
• Main Authors: Naima Ahmed Fahmi, Jae-Woong Chang, Nassereddeen, Heba, Khandakar, Tanvir Ahmed, Fan, Deliang, Jeongsik Yong, Zhang, Wei
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 20.02.2020
• Subjects: 3' Untranslated regions; Bioinformatics; Gene expression; Genomes; Isoforms; miRNA; mRNA processing; Polyadenylation; Post-transcription; RNA-binding protein
• DOI: 10.1101/2020.02.16.951657

The eukaryotic genome is capable of producing multiple isoforms from a gene by alternative polyadenylation (APA) during pre-mRNA processing. APA in the 3'-untranslated region (3'-UTR) of mRNA produces transcripts with shorter 3'-UTR. Often, 3'-UTR serves as a binding platform for microRNAs and RNA-binding proteins, which affect the fate of the mRNA transcript. Thus, 3'-UTR APA provides a means to regulate gene expression at the post-transcriptional level and is known to promote translation. Current bioinformatics pipelines have limited capability in profiling 3'-UTR APA events due to incomplete annotations and a low-resolution analysing power: widely available bioinformatics pipelines do not reference actionable polyadenylation (cleavage) sites but simulate 3'-UTR APA only using RNA-seq read coverage, causing false positive identifications. To overcome these limitations, we developed APA-Scan, a robust program that identifies 3'-UTR APA events and visualizes the RNA-seq short-read coverage with gene annotations. APA-Scan utilizes either predicted or experimentally validated actionable polyadenylation signals as a reference for polyadenylation sites and calculates the quantity of long and short 3'-UTR transcripts in the RNA-seq data. The performance of APA-Scan was validated by qPCR. Footnotes * The references are updated in this revision. * https://github.com/compbiolabucf/APA-Scan