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Related Concept Videos

Restriction Enzymes01:11

Restriction Enzymes

Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called restriction sites. Such palindromic DNA sequences or inverted repeats are commonly found in regions of functional significance, such as the origin of replication, gene operator sites, and regions containing transcription termination signals.
The host bacteria protect their own genomic DNA from these enzymes by methylating these sites. Some...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

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Related Experiment Video

Updated: Jun 28, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Using shotgun sequence data to find active restriction enzyme genes.

Yu Zheng1, Janos Posfai, Richard D Morgan

  • 1New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.

Nucleic Acids Research
|November 8, 2008
PubMed
Summary
This summary is machine-generated.

Analyzing whole genome shotgun sequences can identify lethal genes in Escherichia coli, including active restriction enzyme genes. This method reliably detects these genes in new genomes, aiding functional annotation.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Whole genome shotgun sequencing is a standard method for genome determination.
  • Shotgun cloning experiments reveal genome segments that can or cannot be cloned in Escherichia coli.
  • Identifying genes lethal to E. coli is crucial for understanding genome function and stability.

Purpose of the Study:

  • To establish a reliable method for detecting active restriction enzyme genes in newly sequenced genomes.
  • To facilitate functional annotation of genomes by identifying potentially lethal genes.
  • To demonstrate the utility of whole genome shotgun sequence analysis for identifying restriction enzyme genes.

Main Methods:

  • Analysis of whole genome shotgun sequence datasets.
  • Identification of genes lethal to Escherichia coli during the cloning process.
  • Biochemical validation of identified restriction enzyme activity.

Main Results:

  • Whole genome shotgun sequence analysis successfully identified genes lethal to E. coli.
  • Active restriction enzyme genes were detected in the genomes of Methanocaldococcus jannaschii, Bacillus cereus ATCC 10987, and Methylococcus capsulatus.
  • The activity of these identified restriction enzyme genes was confirmed biochemically.

Conclusions:

  • Whole genome shotgun sequence analysis is a reliable approach for detecting active restriction enzyme genes.
  • This method aids in the functional annotation of newly sequenced genomes.
  • The identification of restriction enzymes provides insights into genome defense mechanisms and evolutionary processes.