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Related Concept Videos

Operons02:09

Operons

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Prokaryotes can control gene expression through operons—DNA sequences consisting of regulatory elements and clustered, functionally related protein-coding genes. Operons use a single promoter sequence to initiate transcription of a gene cluster (i.e., a group of structural genes) into a single mRNA molecule. The terminator sequence ends transcription. An operator sequence, located between the promoter and structural genes, prohibits the operon’s transcriptional activity if bound by...
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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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Inducible Operons: lac Operon01:25

Inducible Operons: lac Operon

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The lac operon in Escherichia coli is a model for understanding inducible gene regulation and metabolic flexibility. It integrates local control by lactose and global regulation through catabolite repression, enabling E. coli to preferentially metabolize glucose when available and switch to lactose utilization when glucose is scarce.Structure and Function of the lac OperonThe lac operon contains three structural genes: lacZ (β-galactosidase), lacY (lactose permease), and lacA...
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Repressible Operon: trp Operon01:21

Repressible Operon: trp Operon

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The trp operon in Escherichia coli exemplifies a repressible operon. It regulates the synthesis of tryptophan through repressor-mediated transcriptional control and attenuation. This dual regulatory mechanism ensures tryptophan biosynthesis occurs only when needed, conserving cellular resources.Structure of the trp OperonThe trp operon consists of five structural genes (trpE, trpD, trpC, trpB, and trpA) that encode enzymes for tryptophan biosynthesis. These genes are transcribed as a single...
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Operon Model01:23

Operon Model

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The operon model represents a fundamental mechanism of gene regulation in prokaryotes, enabling coordinated expression of genes involved in related metabolic or functional pathways. Operons consist of structural genes, a promoter, and an operator, with transcription regulated by repressors, activators, and small effector molecules.Structure and Function of OperonsAn operon is a cluster of structural genes transcribed together under the control of a single promoter. The promoter region...
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RNA Splicing01:32

RNA Splicing

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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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Related Experiment Video

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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A computational system for identifying operons based on RNA-seq data.

Brian Tjaden1

  • 1Department of Computer Science, Wellesley College, Wellesley, MA 02481, USA.

Methods (San Diego, Calif.)
|April 7, 2019
PubMed
Summary
This summary is machine-generated.

This study introduces a new computational system using RNA-sequencing (RNA-seq) data to accurately identify bacterial operons. The method combines genomic data with expression data for better gene co-regulation understanding.

Keywords:
BacteriaBioinformaticsOperonPolycistronicRNA-seqTranscription

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Operons are groups of genes transcribed as a single unit, crucial for understanding gene co-regulation and function.
  • The majority of bacterial genes are organized into operons, making their accurate identification essential for biological insights.

Purpose of the Study:

  • To develop and present a computational system for identifying operons using RNA-sequencing (RNA-seq) data.
  • To improve the understanding of gene co-regulation and functional relationships in bacterial genomes.

Main Methods:

  • A computational system was developed that integrates primary genomic sequence information with RNA-seq expression data.
  • A unified probabilistic model was employed to identify operons across a genome.
  • The system was validated by comparing its predictions to existing operon databases and through experimental confirmation.

Main Results:

  • The developed system accurately identifies operons in various species.
  • The method successfully combines genomic and expression data for operon prediction.
  • New operons were identified and experimentally confirmed using this system.

Conclusions:

  • The presented computational system offers a robust method for operon identification using RNA-seq data.
  • This tool aids in deciphering gene co-regulation and functional relationships in bacteria.
  • The system is freely available, promoting further research in bacterial genomics.