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

By Naima Ahmed Fahmi, Jae-Woong Chang, Heba Nassereddeen, Khandakar Tanvir Ahmed, Deliang Fan, Jeongsik Yong, Wei Zhang

Posted 17 Feb 2020
bioRxiv 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 analyzing 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. Implementation APA-Scan is implemented in Python. Source code and a comprehensive user’s manual are freely available at <https://github.com/compbiolabucf/APA-Scan>

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