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...

Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...

You might also read

Related Articles

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

Sort by

Same author

Quantitative RNA pseudouridine landscape reveals dynamic modification patterns and evolutionary conservation across bacterial species.

eLife·2026

Same author

Beyond dormancy: Active DNA repair and protein synthesis drive antibiotic tolerance and enable synergistic eradication.

Microbiological research·2026

Same author

Global transcription factors analyses reveal hierarchy and synergism of regulatory networks and master virulence regulators in <i>Pseudomonas aeruginosa</i>.

eLife·2026

Same author

Deciphering comprehensive profiles of pathogenies and resistome of pork using integrating metagenomic and isolation strategies.

iMetaOmics·2026

Same author

Molecular surveillance of foodborne bacterial pathogens and resistome in food products from Hong Kong.

Microbiology (Reading, England)·2026

Same author

Metagenomic and culture-based genomics reveal virulence and resistance risks in Manila clam microbiomes.

Food microbiology·2026

Search research articles

Related Experiment Video

Updated: Jun 21, 2025

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing.

Lu Tan¹, Zhihao Guo¹, Yanwen Shao¹

¹Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.

Nucleic Acids Research

|July 16, 2024

Summary

Nanopore Direct RNA Sequencing (DRS) effectively analyzes bacterial RNA, enhancing mRNA yields and enabling transcriptome-wide RNA modification mapping for improved bacterial gene expression studies.

More Related Videos

Author Spotlight: Decoding RNA Methylation's Role in Pancreatic Cancer - A Single-Base Resolution Study

Author Spotlight: Decoding RNA Methylation's Role in Pancreatic Cancer - A Single-Base Resolution Study

Published on: July 7, 2023

Nanopore DNA Sequencing for Metagenomic Soil Analysis

Nanopore DNA Sequencing for Metagenomic Soil Analysis

Published on: December 14, 2017

Related Experiment Videos

Last Updated: Jun 21, 2025

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Author Spotlight: Decoding RNA Methylation's Role in Pancreatic Cancer - A Single-Base Resolution Study

Author Spotlight: Decoding RNA Methylation's Role in Pancreatic Cancer - A Single-Base Resolution Study

Published on: July 7, 2023

Nanopore DNA Sequencing for Metagenomic Soil Analysis

Nanopore DNA Sequencing for Metagenomic Soil Analysis

Published on: December 14, 2017

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Bacterial gene expression relies on complex regulatory networks.
Nanopore Direct RNA Sequencing (DRS) offers rapid bacterial RNA analysis but faces challenges with mRNA read yield and RNA modification detection.
Existing methods require optimization for comprehensive bacterial transcriptome and epitranscriptome characterization.

Purpose of the Study:

To enhance Nanopore Direct RNA Sequencing (DRS) for bacterial RNA analysis.
To improve mRNA read yield and enable transcriptome-wide RNA modification mapping.
To reconstruct complex transcriptome architectures and identify RNA modifications in bacteria.

Main Methods:

Bacterial total RNA underwent pre-processing: size selection, ribosomal RNA depletion, and polyadenylation.
Nanopore DRS was performed on processed RNA from Escherichia coli and Staphylococcus aureus.
Nanopore-based computational tools and Next-Generation Sequencing methods were used for transcriptome and epitranscriptome analysis.

Main Results:

Pre-processing significantly increased sequencing data throughput and mRNA reads.
Complex transcriptome architectures were reconstructed, extending known operon boundaries for E. coli and S. aureus.
Putative RNA modification sites were detected, with 75 high-confidence N6-methyladenosine (m6A) candidates identified in E. coli.

Conclusions:

Optimized Nanopore DRS protocols enhance bacterial mRNA yield and enable comprehensive transcriptome analysis.
The study demonstrates the potential of Nanopore DRS for global RNA modification mapping in bacteria.
This approach provides a systematic and convenient platform for bacterial epitranscriptome studies.