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Related Concept Videos

CRISPR01:59

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Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced...
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The CRISPR-Cas system serves as a bacterial defense mechanism against invading genetic elements such as viruses and plasmids, forming the foundation for its adaptation as a powerful genome-editing tool. Originally discovered in prokaryotes, this system has been repurposed to revolutionize genetic engineering across a wide range of organisms, including plants, animals, and humans. The core component, Cas9, is an endonuclease derived from Streptococcus pyogenes, capable of introducing...
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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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The Antiviral System of Bacteria and Archaea: CRISPR01:23

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CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats is a adaptive immune system found in bacteria and archaea that protects against viral infections. This system enables prokaryotic cells to identify, remember, and neutralize foreign genetic elements, primarily bacteriophages, by storing fragments of the invader’s DNA as a genetic memory.The CRISPR immune response begins during an initial infection. Cas (CRISPR-associated) proteins play a central role in this...
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Pooled CRISPR-Based Genetic Screens in Mammalian Cells
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crisprSQL: a novel database platform for CRISPR/Cas off-target cleavage assays.

Florian Störtz1, Peter Minary1

  • 1Department of Computer Science, University of Oxford, Parks Road, Oxford OX1 3QD, UK.

Nucleic Acids Research
|October 21, 2020
PubMed
Summary
This summary is machine-generated.

CRISPR/Cas9 gene editing is promising but has off-target effects. We created crisprSQL, a database to analyze CRISPR/Cas9 cleavage data, improving gene editing safety and research.

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CIRCLE-Seq for Interrogation of Off-Target Gene Editing
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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genetics

Background:

  • CRISPR/Cas9 technology offers therapeutic gene editing potential.
  • Off-target effects are a significant barrier to clinical applications.
  • Existing off-target cleavage datasets lack a unified, accessible overview.

Purpose of the Study:

  • To present crisprSQL, an interactive database for CRISPR/Cas9 off-target cleavage studies.
  • To provide a comprehensive resource for gene editing safety analysis and transcriptomics.
  • To facilitate research in cleavage profiling and computational off-target prediction.

Main Methods:

  • Developed crisprSQL, an interactive, bioinformatically enhanced collection of off-target cleavage data.
  • Curated data from 144 guide RNAs and 25,632 guide-target pairs from human and rodent cell lines.
  • Included interaction-specific references to epigenetic markers and gene names.

Main Results:

  • crisprSQL offers a transparent overview of CRISPR/Cas9 off-target cleavage studies.
  • The database contains extensive data on guide RNAs, target pairs, and associated genomic features.
  • Provides a foundation for enhanced safety quantification and experimental design.

Conclusions:

  • crisprSQL is the first curated database of its kind for CRISPR/Cas9 off-target cleavage.
  • It will significantly enhance research into gene editing safety and computational prediction models.
  • Facilitates informed experimental design and advances the field of therapeutic gene editing.