Benchmarking of methods that identify alternative polyadenylation events in single-/multiple-polyadenylation site genes.

ABSTRACT: Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that diversifies gene expression by generating messenger RNA isoforms with varying 3' untranslated regions. Accurate identification and quantification of transcriptome-wide polyadenylation site (PAS) usage are essential for understanding APA-mediated gene regulation and its biological implications. In this review, we first review the landscape of computational tools developed to identify APA events from RNA sequencing (RNA-seq) data. We then benchmarked five PAS prediction tools and seven APA detection algorithms using five RNA-seq datasets derived from clear cell renal cell carcinoma (ccRCC) and adjacent normal tissues. By evaluating tool performance across genes with either single or multiple PASs, we reveal

SUBMITTER: Tian Q 

PROVIDER: S-EPMC12076406 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature