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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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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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CRISPR01:59

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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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Chromatin Immunoprecipitation- ChIP02:36

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Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
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ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
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Genetic Screens02:46

Genetic Screens

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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
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Related Experiment Video

Updated: Dec 20, 2025

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
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Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling.

Rachel E Yan1,2,3,4, Alba Corman1,2, Lyla Katgara1,2

  • 1New York Genome Center, New York, NY, USA.

Nature Biotechnology
|November 21, 2024
PubMed
Summary

We developed MultiPerturb-seq, a new CRISPR screening method that measures gene expression and chromatin accessibility simultaneously. This approach identified ZNHIT1 as a potential target for cancer reprogramming therapy.

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Area of Science:

  • Single-cell genomics
  • CRISPR screening
  • Cancer biology

Background:

  • Previous pooled CRISPR screens analyzed gene expression or chromatin accessibility separately.
  • Integrating multiple single-cell modalities presents a technical challenge.

Purpose of the Study:

  • To develop a high-throughput CRISPR screening platform enabling joint analysis of chromatin accessibility, transcriptome, and guide RNA.
  • To apply this platform to identify therapeutic targets in rare pediatric cancers.

Main Methods:

  • MultiPerturb-seq integrates combinatorial indexing and droplet microfluidics.
  • It captures single-nucleus chromatin accessibility, transcriptome, and guide RNA simultaneously.
  • This method significantly scales throughput for multi-modal screening.

Main Results:

  • We successfully integrated three single-cell modalities (chromatin accessibility, transcriptome, guide RNA) in a high-throughput CRISPR screen.
  • Key gene regulators involved in cellular differentiation were identified.
  • ZNHIT1 was identified as a potential therapeutic target for cancer reprogramming.

Conclusions:

  • MultiPerturb-seq offers a powerful new tool for multi-modal pooled CRISPR screening.
  • The identified genes and ZNHIT1 provide new avenues for understanding and treating rare pediatric cancers.