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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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RNA-seq03:21

RNA-seq

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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...
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Translation in Prokaryotes01:29

Translation in Prokaryotes

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Prokaryote translation is a complex, highly coordinated process that converts genetic information from mRNA into functional proteins. It involves three stages: initiation, elongation, and termination, each facilitated by specific molecular components.Initiation of TranslationThe process begins with the assembly of the ribosomal subunits and initiation factors on the mRNA. In bacteria, the 30S ribosomal subunit recognizes the Shine-Dalgarno sequence in the mRNA, a conserved region upstream of...
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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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Coordination of Gene Expression Processes in Bacteria01:29

Coordination of Gene Expression Processes in Bacteria

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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...
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Translational Regulation01:29

Translational Regulation

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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,...
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Related Experiment Video

Updated: Aug 12, 2025

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
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RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing

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Flow-Seq Method: Features and Application in Bacterial Translation Studies.

E S Komarova1, O A Dontsova2,3,4,5, D V Pyshnyi6

  • 1Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, 119234 Russia.

Acta Naturae
|January 25, 2023
PubMed
Summary
This summary is machine-generated.

Flow-seq is a powerful method for analyzing gene expression regulation. It uses reporter constructs and sequencing to identify patterns that enhance protein synthesis efficiency across many mRNA variants.

Keywords:
Flow-seqNGSbacteriaflow cytometryhigh-throughput sequencingtranslation

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Last Updated: Aug 12, 2025

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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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Area of Science:

  • Molecular Biology
  • Genetics
  • Biotechnology

Background:

  • Gene expression regulation is complex, involving various DNA elements.
  • Evaluating the efficiency of multiple mRNA variants simultaneously is challenging.
  • Reporter assays are common but can be limited in scale.

Purpose of the Study:

  • To review and analyze the Flow-seq method for evaluating mRNA translation efficiency.
  • To compare Flow-seq with alternative approaches for assessing expression efficiency.
  • To highlight the capabilities and applications of Flow-seq.

Main Methods:

  • Utilizes reporter construct libraries with thousands of variants.
  • Involves introducing constructs into cells and sorting by fluorescence.
  • Employs next-generation sequencing to analyze sequence-function relationships.

Main Results:

  • Identifies sequence patterns that determine gene expression efficiency.
  • Enables simultaneous evaluation of numerous mRNA variants.
  • Demonstrates the broad applicability of Flow-seq beyond protein synthesis.

Conclusions:

  • Flow-seq is an effective high-throughput method for dissecting gene expression regulation.
  • The method offers a scalable approach to understanding sequence-function dynamics.
  • Flow-seq provides valuable insights into mRNA translation efficiency and beyond.