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Related Concept Videos

RNA-seq03:21

RNA-seq

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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. 
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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.
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Related Experiment Video

Updated: Jan 10, 2026

A Novel Microdissection Approach to Recovering Mycobacterium tuberculosis Specific Transcripts from Formalin Fixed Paraffin Embedded Lung Granulomas
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Transcript-Capture sequencing enriches mRNA of Mycobacterium tuberculosis from host samples.

Eleanor I Lamont1, Richard M Jones1,2, Jessica Assadi1

  • 1Department of Microbiology, University of Washington, Seattle, WA, 98195, USA.

Biorxiv : the Preprint Server for Biology
|November 24, 2025
PubMed
Summary

This study introduces Transcript-Capture Seq, a novel method to analyze bacterial gene expression in clinical samples. It significantly enhances bacterial mRNA detection, enabling the first complete in vivo transcriptome analysis of Mycobacterium tuberculosis in TB patients.

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Area of Science:

  • Microbiology
  • Genomics
  • Infectious Diseases

Background:

  • Studying bacterial gene expression at infection sites is challenging due to low bacterial mRNA levels in clinical samples.
  • Understanding bacterial activity in vivo is crucial for deciphering disease progression and treatment response.

Purpose of the Study:

  • To develop and validate a novel method, Transcript-Capture Seq, for enriching bacterial RNA from host samples.
  • To enable comprehensive analysis of the bacterial transcriptome directly from clinical specimens.
  • To investigate the in vivo gene expression profile of Mycobacterium tuberculosis in tuberculosis patients.

Main Methods:

  • Transcript-Capture Seq utilizes custom biotinylated probes to enrich bacteria-specific RNA.
  • The enriched RNA is then analyzed using Next Generation Sequencing (NGS).
  • The method was applied to both tuberculosis infection models and clinical sputum samples.

Main Results:

  • Transcript-Capture Seq achieved >200-fold enrichment of bacterial mRNA from mixed samples.
  • This is the first study to generate a complete in vivo bacterial transcriptome of Mycobacterium tuberculosis from patient sputum.
  • Mycobacterium tuberculosis in patient sputum showed upregulated genes related to host lipid utilization and zinc limitation, mirroring in vitro log-phase growth.

Conclusions:

  • Transcript-Capture Seq is an effective method for analyzing bacterial gene expression directly from clinical samples.
  • The study provides novel insights into the in vivo physiological state and activity of Mycobacterium tuberculosis in patients.
  • This approach can be instrumental in understanding bacterial adaptation and survival during infection.