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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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CRISPR01:59

CRISPR

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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: May 7, 2026

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors
09:22

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors

Published on: February 28, 2021

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Feature representation for explainable CRISPR off-target prediction and base editing efficiency.

Faiza Hasin1,2, Michele Minervini1, Corrado Mencar1,2

  • 1Department of Computer Science, University of Bari Aldo Moro, Bari, Italy.

Frontiers in Bioinformatics
|May 6, 2026
PubMed
Summary
This summary is machine-generated.

Feature representation impacts CRISPR/Cas9 gene editing prediction accuracy. One-hot encoding excels in base editing, while optimal methods vary for gene knockout, highlighting the importance of sequence features for predicting CRISPR efficacy.

Keywords:
CRISPR/Cas9XGBoostbase editingexplainabilityfeature representationoff-target predictionshap

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

  • Molecular Biology
  • Bioinformatics
  • Gene Editing Technologies

Background:

  • CRISPR/Cas9 gene editing efficacy relies on guide RNA-target DNA interactions.
  • Accurate prediction models require biological insight beyond high accuracy.
  • Off-target prediction is crucial for safe and effective CRISPR applications.

Purpose of the Study:

  • To analyze the impact of feature representation on accuracy and interpretability in CRISPR/Cas9 off-target prediction.
  • To compare different sequence encoding methods for gene knockout and base editing.
  • To evaluate model performance using classification and regression tasks.

Main Methods:

  • Utilized CHANGE-seq, GUIDE-seq, and Hanna screening datasets for gene knockout (KO) and base editing (BE) applications.
  • Employed XGBoost models for both classification and regression prediction tasks.
  • Evaluated paired sequence representations and K-mer encodings.

Main Results:

  • For KO, One-Hot (OH, OH5C) excelled on GUIDE-seq, while Bulges representation was best for CHANGE-seq.
  • One-hot encoding consistently outperformed K-mer for BE prediction accuracy in both tasks.
  • SHapley Additive exPlanations (SHAP) revealed the Protospacer Adjacent Motif (PAM)-proximal region is critical for both KO and BE.

Conclusions:

  • Predictive performance is comparable across gene knockout and base editing, showing framework robustness.
  • Feature representation significantly influences prediction accuracy and interpretability.
  • The PAM-proximal region is a key determinant for CRISPR/Cas9 editing outcomes.