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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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Related Experiment Video

Updated: Sep 6, 2025

Author Spotlight: Exploring the Frontier of mRNA Research with Poly A Tail Analysis Techniques

Author Spotlight: Exploring the Frontier of mRNA Research with Poly A Tail Analysis Techniques

Published on: January 12, 2024

PolyAtailor: measuring poly(A) tail length from short-read and long-read sequencing data.

Mengfei Liu^1,2, Linlin Hao¹, Sien Yang¹

¹Pasteurien College, Soochow University, Suzhou, Jiangsu 215000, China.

Briefings in Bioinformatics

|June 30, 2022

Summary

PolyAtailor is a new tool for analyzing polyadenylation (poly(A)) tail lengths from sequencing data. It offers a unified framework for both long and short reads, improving accuracy and sensitivity in gene expression regulation studies.

Keywords:

RNA processing alternative polyadenylation next generation sequencing polyadenylation tail software third-generation sequencing

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Last Updated: Sep 6, 2025

Author Spotlight: Exploring the Frontier of mRNA Research with Poly A Tail Analysis Techniques

Author Spotlight: Exploring the Frontier of mRNA Research with Poly A Tail Analysis Techniques

Published on: January 12, 2024

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

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

Area of Science:

Molecular Biology
Bioinformatics
Genomics

Background:

The polyadenylation (poly(A)) tail is crucial for eukaryotic gene expression regulation, influencing mRNA export, stability, and translation.
High-throughput sequencing enables transcriptome-wide poly(A) tail profiling, but a universal tool for diverse sequencing protocols is lacking.

Purpose of the Study:

To develop PolyAtailor, a unified and efficient computational framework for identifying and analyzing poly(A) tails from various sequencing data types.
To provide a versatile tool for poly(A) tail and poly(A) site analyses, including differential length analysis and base composition statistics.

Main Methods:

PolyAtailor was established as a framework for analyzing poly(A) tails from PacBio long reads and next-generation short reads.
It includes Tail_map and Tail_scan functions for profiling poly(A) tails with or without a reference genome.
The tool identifies tail position, length, sequence, and type, and integrates functions for differential analysis, site identification, and visualization.

Main Results:

PolyAtailor demonstrated effectiveness in measuring poly(A) tail length and detecting differential poly(A) length.
Comparative analysis showed PolyAtailor achieved higher sensitivity and accuracy than FLAMAnalysis, FLEPSeq, and PAIsoSeqAnalysis using data from HeLa and Arabidopsis samples.
The tool successfully processed data from three different sequencing protocols.

Conclusions:

PolyAtailor provides a universal and efficient solution for poly(A) tail analysis across different sequencing strategies.
Its enhanced accuracy and sensitivity offer significant advantages for studying gene expression regulation.
The framework is publicly available, facilitating broader research in transcriptomics.