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In Situ Capture of Chromatin Interactions by Biotinylated dCas9
Xin Liu1, Yuannyu Zhang1, Yong Chen2
1Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
Cell
|August 26, 2017
Summary
Researchers developed a new CRISPR affinity purification in situ of regulatory elements (CAPTURE) method to identify unknown protein complexes and DNA interactions at specific genomic locations. This approach reveals how cis-regulatory elements control gene expression in development and disease.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- Cis-regulatory elements (CREs) are crucial for gene regulation but their molecular composition is largely unknown.
- Existing methods often rely on correlative chromatin features, limiting discovery of novel regulatory factors.
Purpose of the Study:
- To develop an unbiased method for identifying locus-specific chromatin-regulating protein complexes and long-range DNA interactions.
- To investigate the composition and function of CREs in human development and disease.
Main Methods:
- CRISPR affinity purification in situ of regulatory elements (CAPTURE) using a biotinylated, nuclease-deficient Cas9 and guide RNAs.
- High-resolution, selective isolation of chromatin interactions at single-copy genomic loci.
- Application to human telomeres, β-globin gene enhancers, and disease-associated cis-elements.
Main Results:
- CAPTURE successfully identified known and novel telomeric factors.
- Demonstrated composition-based hierarchical organization of enhancer clusters.
- Revealed spatial features of CREs that causally control gene transcription in development and disease.
Conclusions:
- The CAPTURE approach provides a powerful tool for unbiased, comprehensive analysis of locus-specific regulatory composition.
- This method offers mechanistic insights into genome structure and function, impacting our understanding of development and disease.
