Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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...

Viruses with RNA Genomes

Viruses with RNA Genomes

RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Common Strategies Governing Temperate Phage and α-Herpesvirus Persistence.

Annual review of microbiology·2026

Same author

Extended poly(A) tails are a shared feature of herpesvirus mRNAs.

PLoS pathogens·2026

Same author

Herpes simplex virus 1 fluidizes the nucleus, enabling condensate formation.

Molecular cell·2026

Same author

Defining expansions and perturbations to the RNA polymerase III transcriptome and epitranscriptome by modified direct RNA nanopore sequencing.

Nature communications·2026

Same author

Extended poly(A) tails are a shared feature of herpesvirus mRNAs.

bioRxiv : the preprint server for biology·2025

Same author

Transcriptional consequences of herpes simplex virus 1 ICP4 inducible expression in uninfected cells.

bioRxiv : the preprint server for biology·2025

Search research articles

Related Experiment Video

Updated: Dec 24, 2025

Unbiased Deep Sequencing of RNA Viruses from Clinical Samples

Unbiased Deep Sequencing of RNA Viruses from Clinical Samples

Published on: July 2, 2016

Using Direct RNA Nanopore Sequencing to Deconvolute Viral Transcriptomes.

Daniel P Depledge¹, Angus C Wilson²

¹Department of Medicine, New York University School of Medicine, New York, New York.

Current Protocols in Microbiology

|April 8, 2020

Summary

Long-read nanopore sequencing offers a streamlined method for analyzing complex viral transcriptomes. This approach simplifies RNA analysis, enabling a comprehensive understanding of viral replication and host interactions.

Keywords:

DNA virus RNA sequencing annotation herpesvirus nanopore viral transcriptome

More Related Videos

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Published on: July 27, 2018

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Related Experiment Videos

Last Updated: Dec 24, 2025

Unbiased Deep Sequencing of RNA Viruses from Clinical Samples

Unbiased Deep Sequencing of RNA Viruses from Clinical Samples

Published on: July 2, 2016

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Published on: July 27, 2018

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Area of Science:

Virology
Genomics
Molecular Biology

Background:

Viral genomes encode complex transcriptomes crucial for replication and host interaction.
Short-read sequencing faces challenges in analyzing overlapping viral transcripts and introduces biases.
Analyzing 5' and 3' RNA ends often requires separate, costly methodologies.

Purpose of the Study:

To present a simplified method for full-length viral RNA sequencing using direct RNA sequencing (dRNA-seq).
To provide a guide for generating and analyzing direct RNA sequencing libraries from virus-infected cells.
To enable comprehensive annotation of viral transcriptomes, including modifications and poly(A) tail lengths.

Main Methods:

Utilizing direct RNA sequencing (dRNA-seq) with Oxford Nanopore Technologies on herpes simplex virus (HSV)-infected cells.
Preparing and sequencing dRNA-seq libraries from native RNA to minimize recoding biases.
Developing computational methods for processing, aligning, and analyzing dRNA-seq datasets for transcriptome annotation.

Main Results:

Demonstrated the feasibility of dRNA-seq for full-length viral RNA analysis in a single assay.
Successfully generated high-quality annotation of the HSV transcriptome.
Enabled advanced analyses like poly(A) tail length estimation and RNA modification detection.

Conclusions:

Direct RNA sequencing provides a powerful, unbiased approach to characterizing viral transcriptomes.
This method simplifies the study of viral RNA complexity and host interactions.
The provided protocols facilitate comprehensive viral transcriptome analysis.