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Related Concept Videos

CRISPR/Cas9 Genome Editing01:28

CRISPR/Cas9 Genome Editing

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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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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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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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GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes.

Ravin Poudel1,2, Lidimarie Trujillo Rodriguez2, Christopher R Reisch2

  • 1Genomics and Bioinformatics Research Unit, USDA Agricultural Research Service, Gainesville, FL 32608, USA.

Gigascience
|April 2, 2022
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Summary

GuideMaker rapidly designs guide RNAs (gRNAs) for CRISPR-Cas gene editing in any organism, including non-model species. This tool accelerates genome-wide screens by efficiently identifying effective gRNAs for diverse Cas enzymes.

Keywords:
CRISPR-CasHierarchical Navigable Small World graphPAMPerturb-seqgRNA

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Area of Science:

  • Genetics
  • Molecular Biology
  • Bioinformatics

Background:

  • CRISPR-Cas systems offer powerful gene editing capabilities in various organisms.
  • Existing guide RNA (gRNA) design tools are often limited to model organisms and standard Cas enzymes.
  • Challenging gene editing projects require specialized tools for non-standard enzymes or non-model organisms.

Purpose of the Study:

  • To develop a fast and user-friendly tool, GuideMaker, for designing CRISPR-Cas guide RNAs (gRNAs).
  • To enable efficient genome-wide gRNA design for challenging applications, including non-standard Cas enzymes and non-model organisms.
  • To facilitate the design of gRNA panels for large-scale genetic screens.

Main Methods:

  • GuideMaker utilizes degenerate protospacer-adjacent motif (PAM) and genome data for rapid gRNA design.
  • The tool employs hierarchical navigable small world graphs to accelerate gRNA comparisons.
  • On-target and off-target scoring options are available to ensure gRNA efficacy.

Main Results:

  • GuideMaker can design gRNAs for all genes in a bacterial genome in approximately 1-2 minutes.
  • The software supports genome-wide gRNA design for any CRISPR-Cas enzyme, including in non-model organisms.
  • Both prokaryotic and eukaryotic genomes can be efficiently processed by GuideMaker.

Conclusions:

  • GuideMaker provides a versatile solution for rapid genome-wide gRNA design across diverse biological systems.
  • The tool supports non-model organisms and non-standard Cas enzymes, expanding CRISPR applications.
  • GuideMaker is accessible as command-line software, a web application, and within the CyCverse Discovery Environment.