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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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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.
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...
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Types of RNA01:23

Types of RNA

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Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
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Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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Leaky Scanning02:28

Leaky Scanning

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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

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Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
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Riboswitches01:56

Riboswitches

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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
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Related Experiment Video

Updated: Jul 5, 2025

Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling
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Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling

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Ribosome Profiling Methods Adapted to the Study of RNA-Dependent Translation Regulation in Staphylococcus aureus.

Maximilian P Kohl1, Béatrice Chane-Woon-Ming1, Roberto Bahena-Ceron1

  • 1Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France.

Methods in Molecular Biology (Clifton, N.J.)
|January 13, 2024
PubMed
Summary
This summary is machine-generated.

This study adapts ribosome profiling to understand how small regulatory RNAs (sRNAs) control gene expression in Staphylococcus aureus. This method offers a genome-wide view of translational regulation crucial for bacterial adaptation and pathogenicity.

Keywords:
Ribo-RETRibo-seqRibosome profilingStaphylococcus aureusStart codonsTranslation initiationTranslation regulation

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Area of Science:

  • Microbiology
  • Molecular Biology
  • Genomics

Background:

  • Noncoding RNAs, including regulatory RNAs (sRNAs), are key regulators of gene expression in pathogenic bacteria like Staphylococcus aureus.
  • sRNAs modulate bacterial adaptation to host environments by controlling virulence factor synthesis and pathogenicity.
  • RNA modifications in ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) may also contribute to stress adaptation.

Purpose of the Study:

  • To adapt and describe protocols for performing ribosome profiling in Staphylococcus aureus.
  • To provide a genome-wide perspective on translational regulation mediated by noncoding RNAs.
  • To enhance understanding of Staphylococcus aureus physiopathology and RNA-mediated gene expression control.

Main Methods:

  • Adaptation of ribosome profiling protocols for application in Staphylococcus aureus.
  • Genome-wide sequencing approaches to analyze translational regulation.
  • Characterization of the landscape of translational regulation.

Main Results:

  • Established protocols for ribosome profiling in Staphylococcus aureus.
  • Enabled genome-wide analysis of translational regulation.
  • Provided a foundation for deeper understanding of RNA-dependent gene expression.

Conclusions:

  • Ribosome profiling is a powerful tool for studying RNA-mediated translational regulation in Staphylococcus aureus.
  • This methodology facilitates a comprehensive understanding of bacterial adaptation and pathogenicity.
  • Further research can leverage these protocols to explore sRNA functions and stress responses.