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Related Concept Videos

Translational Regulation01:29

Translational Regulation

Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
Transcriptional Regulation: Riboswitches01:23

Transcriptional Regulation: Riboswitches

Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
General Transcription Factors01:30

General Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Riboswitches01:56

Riboswitches

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...
Transcription Factors02:16

Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...

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Related Experiment Video

Updated: May 24, 2026

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria
08:34

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria

Published on: February 23, 2021

Multiple factors dictate target selection by Hfq-binding small RNAs.

Chase L Beisel1, Taylor B Updegrove, Ben J Janson

  • 1Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA. cbeisel@ncsu.edu

The EMBO Journal
|March 6, 2012
PubMed
Summary

Bacterial small RNAs (sRNAs) regulate gene expression by binding to messenger RNAs (mRNAs). This study reveals that specific features of sRNAs, particularly their unstructured regions, are crucial for effective target recognition and regulation.

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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

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Last Updated: May 24, 2026

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria
08:34

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria

Published on: February 23, 2021

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
12:24

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

Area of Science:

  • Bacterial molecular biology
  • Gene regulation mechanisms
  • RNA-RNA interactions

Background:

  • Bacterial small RNAs (sRNAs) bind to messenger RNAs (mRNAs) to control their stability and translation.
  • The precise rules governing which mRNAs are targeted by sRNAs, especially those involving Hfq protein, are not fully understood.
  • Identifying target specificity is crucial for understanding bacterial stress responses and gene networks.

Purpose of the Study:

  • To elucidate the key features determining target selection by Hfq-binding sRNAs.
  • To improve the prediction of sRNA targets using the Escherichia coli sRNA Spot 42 as a model system.
  • To understand the structural and sequence requirements for sRNA-mediated gene regulation.

Main Methods:

  • Utilized computational predictions focusing on unstructured regions of the sRNA Spot 42 to identify potential mRNA targets.
  • Experimentally validated predicted targets and investigated the impact of base-pairing extent and location on regulatory efficiency.
  • Analyzed structural features of non-target mRNAs, including Hfq-binding sites and secondary structure occlusions, and experimentally modified these features.

Main Results:

  • Focusing predictions on unstructured regions of Spot 42 significantly improved the identification of both known and novel mRNA targets.
  • Enhanced base-pairing in unstructured regions correlated with stronger gene regulation, while base-pairing in structured regions had less impact.
  • Non-target mRNAs often lacked Hfq-binding sites, possessed occluding secondary structures, or had overlapping binding and targeting sites, which could be modified to enable regulation.

Conclusions:

  • Unstructured regions of Hfq-binding sRNAs are critical determinants for accurate target recognition and efficient gene regulation.
  • The presence and accessibility of Hfq-binding sites on both sRNAs and target mRNAs are essential for effective regulation.
  • These findings provide a refined framework for predicting sRNA targets and understanding the principles of sRNA-mediated gene control in bacteria.