APA-Scan: detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data.
BMC Bioinformatics
; 23(Suppl 3): 396, 2022 Sep 28.
Article
em En
| MEDLINE
| ID: mdl-36171568
ABSTRACT
BACKGROUND:
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 or longer 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 is known to modulate translation and provides a mean to regulate gene expression at the post-transcriptional level. 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.METHODS:
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. APA-Scan works in three majorsteps:
(i) calculate the read coverage of the 3'-UTR regions of genes; (ii) identify the potential APA sites and evaluate the significance of the events among two biological conditions; (iii) graphical representation of user specific event with 3'-UTR annotation and read coverage on the 3'-UTR regions. APA-Scan is implemented in Python3. Source code and a comprehensive user's manual are freely available at https//github.com/compbiolabucf/APA-Scan .RESULT:
APA-Scan was applied to both simulated and real RNA-seq datasets and compared with two widely used baselines DaPars and APAtrap. In simulation APA-Scan significantly improved the accuracy of 3'-UTR APA identification compared to the other baselines. The performance of APA-Scan was also validated by 3'-end-seq data and qPCR on mouse embryonic fibroblast cells. The experiments confirm that APA-Scan can detect unannotated 3'-UTR APA events and improve genome annotation.CONCLUSION:
APA-Scan is a comprehensive computational pipeline to detect transcriptome-wide 3'-UTR APA events. The pipeline integrates both RNA-seq and 3'-end-seq data information and can efficiently identify the significant events with a high-resolution short reads coverage plots.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Poliadenilação
/
MicroRNAs
Tipo de estudo:
Diagnostic_studies
Limite:
Animals
Idioma:
En
Revista:
BMC Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2022
Tipo de documento:
Article
País de afiliação:
Estados Unidos