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Ribosome Profiling02:24

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 helps...

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A Duplex Digital PCR Assay for Simultaneous Quantification of the Enterococcus spp. and the Human Fecal-associated HF183 Marker in Waters
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A simple and efficient method to search for selected primary transcripts: non-coding and antisense RNAs in the human

Aymeric Fouquier d'Hérouel1, Françoise Wessner, David Halpern

  • 1INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France.

Nucleic Acids Research
|January 27, 2011
PubMed
Summary

This study introduces 5'tagRACE, a novel method for discovering bacterial non-coding RNAs (ncRNAs) in Enterococcus faecalis. Researchers identified 29 new ncRNAs, advancing our understanding of bacterial gene regulation and pathogenicity.

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A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae

Published on: April 25, 2015

Area of Science:

  • Microbiology
  • Genomics
  • Molecular Biology

Background:

  • Enterococcus faecalis is a common bacterium and a significant human pathogen.
  • Understanding its genetic makeup, particularly non-coding RNAs (ncRNAs), is crucial for studying its pathogenicity.

Purpose of the Study:

  • To conduct the first comprehensive search for ncRNAs on the E. faecalis chromosome.
  • To introduce and validate a novel method, 5'tagRACE, for ncRNA discovery and characterization.
  • To explore the functional implications of identified ncRNAs and transcriptional organizations.

Main Methods:

  • In silico predictions were combined with a novel 5'RACE-derivative method called '5'tagRACE'.
  • The 5'tagRACE method was used to probe and characterize primary transcripts simultaneously.
  • Analysis focused on 45 selected loci across the E. faecalis chromosome.

Main Results:

  • Discovery and mapping of 29 novel ncRNAs in E. faecalis.
  • Identification of 10 putative novel messenger RNAs (mRNAs).
  • Characterization of 16 antisense transcriptional organizations, including an ncRNA antisense to SsrS and insights into toxin-antitoxin modules.

Conclusions:

  • The 5'tagRACE method is simple, reliable, and sensitive for bacterial ncRNA discovery.
  • The study significantly expands the known ncRNA landscape of E. faecalis.
  • Identified ncRNAs and transcriptional organizations offer new avenues for understanding E. faecalis virulence and gene regulation.