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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Updated: Sep 15, 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

APALORD: An R-based tool for differential alternative polyadenylation analysis of long-read RNA-seq data.

Zhiping Zhang¹, Heather Glatt-Deeley¹, Lehan Zou²

¹Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA.

Biorxiv : the Preprint Server for Biology

|July 16, 2025

Summary

APALORD is a new R tool for analyzing alternative polyadenylation (APA) in long-read RNA sequencing data. It accurately identifies polyadenylation sites and quantifies usage, revealing 3'UTR dynamics in various cell types and tissues.

Keywords:

Alternative polyadenylation (APA)differential APA long-read (LR) RNA-seq polyadenylation site (PAS)

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Last Updated: Sep 15, 2025

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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Published on: June 24, 2021

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

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Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Alternative polyadenylation (APA) generates RNA isoform diversity, impacting gene expression regulation.
Long-read (LR) RNA sequencing offers new possibilities for studying APA mechanisms.
Existing tools may not fully leverage LR RNA-seq data for comprehensive APA analysis.

Purpose of the Study:

To introduce APALORD, an R-based tool for APA analysis of LR RNA-seq data.
To enable precise identification and quantification of polyadenylation sites (PASs) and their usage (PAU).
To facilitate differential APA analysis across various biological conditions and sample types.

Main Methods:

APALORD utilizes precise 3' end information from 3'-primed LR RNA-seq data.
It identifies PASs and quantifies PAU at both gene and individual PAS levels.
Statistical analyses include the Kolmogorov-Smirnov test (gene level) and DEXSeq (PAS level).

Main Results:

APALORD accurately identified PASs in direct RNA-seq data from human embryonic stem cells (hESCs) and derived neurons.
A transcriptome-wide 3'UTR lengthening trend was observed, consistent with prior research.
Analysis of PacBio cDNA and Nanopore R2C2 data revealed 3'UTR lengthening and APA changes associated with polysome fractions.

Conclusions:

APALORD provides a robust framework for differential APA analysis using LR RNA-seq data.
The tool aids in investigating 3' end dynamics in diverse biological contexts.
APALORD empowers researchers to explore APA mechanisms with enhanced precision and scope.