Quantifying alternative polyadenylation in RNAseq data with LABRAT

• Published in: Methods in enzymology Vol. 655; p. 245
• Main Authors: Gillen, Austin E, Goering, Raeann, Taliaferro, J Matthew
• Format: Journal Article
• Language: English
• Published: United States 2021
• Subjects: 3' Untranslated Regions; High-Throughput Nucleotide Sequencing; Polyadenylation; Protein Isoforms; Transcriptome; Alternative polyadenylation; Post-transcriptional regulation; 3′ UTR regulation; Single cell RNAseq; Transcriptomics
• ISSN: 1557-7988
• DOI: 10.1016/bs.mie.2021.03.018

Alternative polyadenylation (APA) generates transcript isoforms that differ in their 3' UTR content and may therefore be subject to different regulatory fates. Although the existence of APA has been known for decades, quantification of APA isoforms from high-throughput RNA sequencing data has been difficult. To facilitate the study of APA in large datasets, we developed an APA quantification technique called LABRAT (Lightweight Alignment-Based Reckoning of Alternative Three-prime ends). LABRAT leverages modern transcriptome quantification approaches to determine the relative abundances of APA isoforms. In this manuscript we describe how LABRAT produces its calculations, provide a step-by-step protocol for its use, and demonstrate its ability to quantify APA in single-cell RNAseq data.