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CRISPR01:59

CRISPR

50.6K
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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Homologous Recombination02:31

Homologous Recombination

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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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CRISPR and crRNAs02:53

CRISPR and crRNAs

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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.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
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Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
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Related Experiment Video

Updated: Jun 24, 2025

Genome Editing in Mammalian Cell Lines using CRISPR-Cas
07:56

Genome Editing in Mammalian Cell Lines using CRISPR-Cas

Published on: April 11, 2019

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Strong association between genomic 3D structure and CRISPR cleavage efficiency.

Shaked Bergman1, Tamir Tuller1,2

  • 1Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel.

Plos Computational Biology
|June 7, 2024
PubMed
Summary

CRISPR gene editing efficiency is linked to 3D genome structure. Lower spatial density predicts higher cleavage, improving CRISPR specificity and therapeutic design.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Biotechnology

Background:

  • CRISPR gene editing offers precise in-vivo genome modification but faces challenges with specificity and sensitivity.
  • Understanding the determinants of CRISPR's on-target and off-target effects is crucial for its advancement.

Purpose of the Study:

  • To investigate the association between chromosomal 3D spatial structure and CRISPR cleavage efficiency.
  • To develop and evaluate 3D-based genomic features for predicting CRISPR activity.

Main Methods:

  • Utilized high-resolution Hi-C data to calculate 3D distances between human genome regions.
  • Generated 3D-based features representing genomic region density.
  • Evaluated these features against empirical in-vivo CRISPR efficiency data and compared them to existing models.

Main Results:

  • 3D spatial features ranked in the top 13% of all evaluated features.
  • Incorporating 3D features significantly enhanced the predictive power of LASSO and xgboost models.
  • Genomic sites with lower 3D spatial density exhibited higher CRISPR cleavage efficiency.

Conclusions:

  • The 3D structure of the genome is a significant determinant of CRISPR cleavage efficiency.
  • These findings offer insights into CRISPR's mechanism and improve the prediction of its activity.
  • The developed 3D features can aid in designing more effective sgRNAs for therapeutic and research applications.