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Updated: Oct 31, 2025

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Quantifying alternative polyadenylation in RNAseq data with LABRAT.

Austin E Gillen¹, Raeann Goering², J Matthew Taliaferro²

¹Division of Hematology, University of Colorado School of Medicine, Aurora, CO, United States.

Methods in Enzymology

|June 29, 2021

Summary

This summary is machine-generated.

Alternative polyadenylation (APA) creates different gene versions, impacting regulation. We developed LABRAT, a new method to accurately quantify these APA isoforms from RNA sequencing data, enabling large-scale studies.

Keywords:

3′ UTR regulation Alternative polyadenylation Post-transcriptional regulation Single cell RNAseq Transcriptomics

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Published on: March 7, 2018

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Alternative polyadenylation (APA) generates transcript isoforms with varying 3' UTRs, influencing gene regulation.
Quantifying APA isoforms from high-throughput RNA sequencing (RNA-seq) data presents significant challenges.
Understanding APA is crucial for deciphering gene expression complexity.

Purpose of the Study:

To develop and present a novel computational method for quantifying APA isoforms.
To enable the efficient and accurate analysis of APA in large-scale RNA-seq datasets.
To provide a user-friendly protocol for researchers studying APA.

Main Methods:

Developed LABRAT (Lightweight Alignment-Based Reckoning of Alternative Three-prime ends), a novel APA quantification technique.
LABRAT utilizes modern transcriptome quantification strategies to determine relative APA isoform abundances.
The method is validated for its ability to quantify APA in single-cell RNA sequencing data.

Main Results:

LABRAT provides a robust and scalable approach for quantifying APA isoforms.
The study details the computational underpinnings of LABRAT's calculations.
Demonstrated successful application of LABRAT to single-cell RNA-seq data, highlighting its versatility.

Conclusions:

LABRAT facilitates the large-scale study of alternative polyadenylation.
This method enhances the ability to investigate the regulatory roles of APA isoforms.
LABRAT is a valuable tool for researchers in transcriptomics and gene regulation.