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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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CRISPR01:59

CRISPR

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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 and crRNAs02:53

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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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RNA Editing02:23

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
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CRISPR-Cas9-Mediated Precise Knock-In Edits in Zebrafish Hearts
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Predictable and precise template-free CRISPR editing of pathogenic variants.

Max W Shen1,2, Mandana Arbab3,4,5, Jonathan Y Hsu6,7

  • 1Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA.

Nature
|November 9, 2018
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Summary

Template-free Cas9 genome editing is now predictable for precise DNA repair. This machine learning approach corrects disease-associated mutations, offering a new tool for gene therapy applications.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • DNA repair after Cas9 cleavage is typically random and unpredictable.
  • This limits its application beyond simple gene disruption.

Purpose of the Study:

  • To demonstrate predictable and precise template-free Cas9 genome editing.
  • To develop a machine learning model for predicting editing outcomes.

Main Methods:

  • Trained a machine learning model, inDelphi, on 2,000 Cas9 guide RNA and DNA target site pairs.
  • inDelphi predicts deletion and insertion genotypes and frequencies.
  • Validated predictions in human and mouse cell lines.

Main Results:

  • inDelphi accurately predicts editing outcomes (r=0.87).
  • Identified Cas9 guide RNAs yielding precise editing (precise-50) in 5-11% of cases.
  • Successfully corrected disease-causing mutations in patient-derived cells (Hermansky-Pudlak syndrome, Menkes disease).

Conclusions:

  • Template-free Cas9 editing can be precise and predictable.
  • inDelphi enables accurate genotype prediction for genome editing.
  • This approach facilitates precise correction of genetic diseases.