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CRISPR01:59

CRISPR

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 Short...
Homologous Recombination02:31

Homologous Recombination

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...
CRISPR and crRNAs02:53

CRISPR and crRNAs

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...
CRISPR01:59

CRISPR

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 Short...
The Antiviral System of Bacteria and Archaea: CRISPR01:23

The Antiviral System of Bacteria and Archaea: CRISPR

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 defense.
CRISPR/Cas9 Genome Editing01:28

CRISPR/Cas9 Genome Editing

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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Related Experiment Video

Updated: Jun 30, 2026

Efficient Production and Identification of CRISPR/Cas9-generated Gene Knockouts in the Model System Danio rerio
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Efficient Production and Identification of CRISPR/Cas9-generated Gene Knockouts in the Model System Danio rerio

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Systematic enhancer mapping and functional analysis in zebrafish with optimized CRISPR interference.

Jiulin Chan1,2, Zhichao Wu1,2, Mingli Liu1,2

  • 1Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.

Nucleic Acids Research
|December 19, 2025
PubMed
Summary
This summary is machine-generated.

Researchers optimized Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) in zebrafish to study gene regulation. This system identified novel enhancers controlling fin and blood cell development, advancing cis-regulatory element annotation.

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Area of Science:

  • Genomics
  • Developmental Biology
  • Molecular Genetics

Background:

  • Noncoding cis-regulatory elements, especially enhancers, are vital for gene expression control.
  • Studying enhancer function in vivo using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) interference (CRISPRi) has been challenging in zebrafish models.

Purpose of the Study:

  • To optimize the CRISPRi system in zebrafish for efficient gene suppression.
  • To functionally annotate distal enhancers of globin genes using the optimized CRISPRi system.
  • To develop an integrated platform for cis-regulatory element annotation in vertebrates.

Main Methods:

  • Optimized CRISPRi system by fine-tuning component concentrations for efficient gene knockdown.
  • Applied CRISPRi to functionally characterize distal enhancers of globin genes.
  • Utilized Hi-C and histone modification assays to map enhancer-promoter (EP) interactions genome-wide.

Main Results:

  • Identified previously unreported enhancers with significant regulatory strength, impacting fin and blood cell development.
  • Mapped 434 enhancer-promoter interactions, revealing novel regulatory loops.
  • Validated several novel EP loops, demonstrating the effectiveness of the integrated approach.

Conclusions:

  • The optimized CRISPRi system enhances functional studies of enhancers in zebrafish.
  • The study provides a robust platform integrating computational and experimental methods for cis-regulatory element annotation.
  • This work advances the understanding of gene regulation in vertebrate development and disease.