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Related Concept Videos

RNA-seq03:21

RNA-seq

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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
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...
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,...
Coordination of Gene Expression Processes in Bacteria01:29

Coordination of Gene Expression Processes in Bacteria

The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...
Stringent Response in E. coli01:23

Stringent Response in E. coli

Bacterial growth is closely tied to nutrient availability, with cells proliferating exponentially under favorable conditions and entering a stationary phase when resources become scarce. This transition is mediated by a regulatory mechanism known as the stringent response, which allows bacteria to adapt to nutrient deprivation by modulating gene expression and metabolic activity.During nutrient scarcity, intracellular amino acid levels decline. It results in the accumulation of uncharged tRNAs...

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Updated: May 9, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
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Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate

Shan Li1, Xia Dong, Zhengchang Su

  • 1Department of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA.

BMC Genomics
|August 1, 2013
PubMed
Summary
This summary is machine-generated.

E. coli K12 exhibits a complex transcriptome with alternative operon forms, antisense RNA, and non-coding RNA. This study used directional RNA-seq and TruHMM to reveal dynamic transcriptional patterns in this model bacterium.

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Last Updated: May 9, 2026

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Probing mRNA Kinetics in Space and Time in Escherichia coli using Two-Color Single-Molecule Fluorescence In Situ Hybridization
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Probing mRNA Kinetics in Space and Time in Escherichia coli using Two-Color Single-Molecule Fluorescence In Situ Hybridization

Published on: July 30, 2020

Area of Science:

  • Microbiology
  • Molecular Biology
  • Genomics

Background:

  • Prokaryotic gene transcription complexity is underestimated.
  • Alternative transcription, antisense RNA (asRNA), and non-coding RNA (ncRNA) are prevalent in many prokaryotes.
  • E. coli K12 transcriptome complexity remains largely uncharacterized.

Purpose of the Study:

  • To comprehensively profile the E. coli K12 transcriptome under various conditions.
  • To investigate alternative operon usage, asRNA, and ncRNA expression.
  • To assess the utility of directional RNA-seq and TruHMM for prokaryotic transcriptome analysis.

Main Methods:

  • Directional RNA-sequencing (RNA-seq) to capture diverse transcripts.
  • Culturing E. coli K12 under different conditions and growth phases.
  • Employing the TruHMM algorithm for accurate full-length transcript assembly.

Main Results:

  • 46.9–63.4% of expressed operons showed alternative forms.
  • 72.23–89.54% of genes had associated asRNA transcripts.
  • 51.37–72.74% of intergenic regions contained ncRNA transcripts.

Conclusions:

  • E. coli K12 possesses a highly complex and dynamic transcriptome.
  • These findings highlight the intricate transcriptional landscape of E. coli.
  • TruHMM is an effective tool for assembling prokaryotic full-length transcripts from RNA-seq data.