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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,...
Types of RNA01:23

Types of RNA

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...
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...
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...
Leaky Scanning02:28

Leaky Scanning

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 stands for...
Experimental RNAi02:15

Experimental RNAi

RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...

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Related Experiment Video

Updated: May 8, 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

Comparative genomics boosts target prediction for bacterial small RNAs.

Patrick R Wright1, Andreas S Richter, Kai Papenfort

  • 1Genetics and Experimental Bioinformatics, Faculty of Biology, Centre for Biological Systems Analysis, and BIOSS Centre for Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany.

Proceedings of the National Academy of Sciences of the United States of America
|August 28, 2013
PubMed
Summary

A new computational strategy, CopraRNA, predicts bacterial small RNA (sRNA) targets and regulatory networks. This method identifies numerous novel sRNA targets and functions, advancing our understanding of gene regulation.

Keywords:
E. coliRNA–RNA interactionregulatory RNA

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Last Updated: May 8, 2026

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Published on: February 23, 2021

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Area of Science:

  • Microbiology
  • Genetics
  • Bioinformatics

Background:

  • Bacterial small RNAs (sRNAs) are crucial gene expression regulators, often targeting multiple mRNAs post-transcriptionally.
  • Identifying sRNA targets experimentally is laborious, hindering a comprehensive understanding of their regulatory roles.

Purpose of the Study:

  • To develop a computational strategy, CopraRNA, for large-scale prediction of sRNA targets and reconstruction of regulatory networks.
  • To precisely predict sRNA domains involved in target recognition and interaction.

Main Methods:

  • CopraRNA integrates phylogenetic information for genomic-scale sRNA target prediction.
  • Functional enrichment and network analysis are employed to reconstruct regulatory networks.
  • The algorithm predicts specific sRNA domains for target interaction.

Main Results:

  • CopraRNA identified additional targets and functions for known sRNAs like CyaR, FnrS, RybB, RyhB, SgrS, and Spot42.
  • Several mRNAs were identified as regulatory hubs targeted by multiple sRNAs.
  • The prediction accuracy of CopraRNA was validated, outperforming traditional experimental methods for some cases.

Conclusions:

  • CopraRNA offers a powerful, efficient, and scalable approach for bacterial sRNA target prediction and network analysis.
  • The tool facilitates high-confidence target prediction and classification of bacterial sRNAs, advancing post-transcriptional regulatory studies.