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Related Concept Videos

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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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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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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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Related Experiment Video

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Gene Digital Circuits Based on CRISPR-Cas Systems and Anti-CRISPR Proteins
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A Simple Criterion for Inferring CRISPR Array Direction.

Ognjen Milicevic1,2, Jelena Repac3, Bojan Bozic3

  • 1School of Medicine, University of Belgrade, Belgrade, Serbia.

Frontiers in Microbiology
|September 26, 2019
PubMed
Summary
This summary is machine-generated.

A new method, Cas Orientation, accurately determines CRISPR array direction for over 95% of cases where standard tools fail. This advance aids research into CRISPR/Cas functions.

Keywords:
CRISPR array orientationCRISPR/Cascas gene orientationlarge-scale analysisnon-canonical functions

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Determining the transcriptional direction of CRISPR arrays is crucial for understanding CRISPR/Cas system functions.
  • Existing methods like CRISPRDirection have limitations, failing to predict orientation for a significant percentage of CRISPR arrays, particularly in subtypes like II-B.
  • Alternative methods may offer fewer undetermined predictions but potentially at the cost of accuracy.

Purpose of the Study:

  • To introduce and evaluate a novel, simple criterion for inferring CRISPR array transcriptional direction: Cas Orientation.
  • To systematically compare the performance of Cas Orientation against established methods (CRISPRDirection and Potential Orientation) across all CRISPR/Cas subtypes.
  • To assess the accuracy and efficiency of Cas Orientation, especially for arrays where other methods yield undetermined predictions.

Main Methods:

  • Proposed Cas Orientation method based on the direction of associated cas genes.
  • Systematic performance assessment across all CRISPR/Cas subtypes.
  • Cross-validation of predictions between Cas Orientation, CRISPRDirection, and Potential Orientation.
  • Comparison against an experimental dataset.

Main Results:

  • Cas Orientation accurately assigns orientation to approximately 95% of CRISPR arrays undetermined by CRISPRDirection.
  • Cas Orientation demonstrates higher accuracy than Potential Orientation and comparable accuracy to CRISPRDirection.
  • CRISPRDirection predictions show better agreement with Cas Orientation than with Potential Orientation.
  • Cas Orientation is simple to implement, requiring only the prediction of associated protein-coding gene direction.

Conclusions:

  • Cas Orientation offers a highly accurate and efficient solution for determining CRISPR array direction, significantly improving upon existing methods.
  • This method enhances the systematic investigation of CRISPR/Cas functions, including non-canonical ones.
  • Cas Orientation's simplicity and high success rate make it a valuable tool for prokaryotic genomics research.