Related Experiment Video
Updated: Aug 20, 2025
09:20
CRISPR-Mediated Reorganization of Chromatin Loop Structure
Published on: September 14, 2018
12.6K
Dissecting Locus-Specific Chromatin Interactions by CRISPR CAPTURE
Giovanni A Botten1,2, Michael Lee1,2, Jian Xu3,4
1Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Methods in Molecular Biology (Clifton, N.J.)
|November 25, 2022
Summary
Researchers developed a CRISPR-based tool called CAPTURE to identify the molecular components and interactions of cis-regulatory elements (CREs) in the genome. This method helps understand how gene expression is controlled in specific tissues.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- Tissue-specific gene expression relies on cis-regulatory elements (CREs) and trans-acting factors.
- Current methods lack detailed understanding of the in situ molecular composition of most CREs.
- Investigating CREs is crucial for understanding gene regulation.
Purpose of the Study:
- To present a detailed protocol for the CRISPR-based CAPTURE (CRISPR affinity purification in situ of regulatory elements) toolbox.
- To enable the interrogation of locus-specific chromatin complexes and configurations.
- To identify the in situ regulatory composition of CREs.
Main Methods:
- Utilizing an in vivo biotinylated nuclease-deficient Cas9 (dCas9) protein.
- Employing programmable single-guide RNAs (sgRNAs) for targeting specific CREs.
- Implementing the CAPTURE toolbox for affinity purification of CRE-associated macromolecular complexes and chromatin looping.
Main Results:
- The CAPTURE toolbox successfully identifies CRE-associated macromolecular complexes.
- The method allows for the detection of chromatin looping interactions.
- Provides a detailed protocol for interrogating the molecular composition of chromatin complexes at specific genomic loci.
Conclusions:
- The CRISPR-based CAPTURE method offers a powerful approach to decipher the molecular intricacies of CREs.
- This technique advances the understanding of gene regulation by characterizing the in situ composition and configuration of regulatory elements.
- The detailed protocol facilitates broader application of CAPTURE in mammalian genomics research.
Related Concept Videos
01:59CRISPR
52.7K
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...
52.7K
02:36Chromatin Immunoprecipitation- ChIP
11.2K
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.
Types of ChIP
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...
Types of ChIP
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...
11.2K
02:53Conservative Site-specific Recombination and Phase Variation
6.1K
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...
The recognition sites for Cre recombinase called LoxP...
6.1K
01:28CRISPR/Cas9 Genome Editing
132
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...
132