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Related Experiment Video

Updated: Jun 21, 2026

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

Published on: May 2, 2025

Transcriptome analysis by strand-specific sequencing of complementary DNA.

Dmitri Parkhomchuk¹, Tatiana Borodina, Vyacheslav Amstislavskiy

¹Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestr. 73, 14195 Berlin, Germany.

Nucleic Acids Research

|July 22, 2009

Summary

This summary is machine-generated.

This study introduces a novel cDNA sequencing method to determine RNA transcript direction. This approach enhances gene structure and expression analysis, aiding in the discovery of new genes and regulatory elements.

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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

High-throughput complementary DNA sequencing (RNA-Seq) is vital for transcriptome analysis, providing data on transcript expression levels and structures.
A key limitation of standard RNA-Seq is the inability to determine transcript polarity, making it challenging to identify the transcribed strand.
Accurate transcript orientation is crucial for a comprehensive understanding of gene expression and regulation.

Purpose of the Study:

To develop and present a straightforward cDNA sequencing protocol that retains transcript directionality information.
To demonstrate the utility of strand-specific RNA sequencing in improving gene structure and expression analysis.
To showcase the application of this method in identifying novel genes and studying transcriptional phenomena like antisense transcription.

Main Methods:

A novel cDNA sequencing protocol was developed to preserve transcript orientation.
The protocol was applied to Saccharomyces cerevisiae and mouse brain transcriptomes.
Transcriptional landscapes were generated and analyzed to assess gene structure, expression, and novel transcript discovery.

Main Results:

The developed protocol successfully preserved transcript directionality.
Strand-specific analysis led to more accurate determination of gene structures and expression levels.
The method facilitated the identification of previously undiscovered genes.
New insights into promoter-associated and antisense transcription were obtained.
Comprehensive transcriptional landscapes are publicly available.

Conclusions:

The novel cDNA sequencing protocol offers a simple yet powerful method for determining transcript polarity.
Understanding transcript orientation significantly improves the accuracy of whole-transcriptome analysis.
This technique is valuable for gene discovery, expression profiling, and the study of complex transcriptional landscapes.