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Updated: Jul 20, 2026
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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
Published on: October 5, 2018
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between
Josée Dostie1, Todd A Richmond, Ramy A Arnaout
1Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605-0103, USA.
Genome Research
|September 7, 2006
Summary
We developed 5C-Carbon Copy (5C), a high-throughput method to map physical interactions between genomic elements. This technique identified new interactions in the human beta-globin locus, aiding gene regulation studies.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- Physical interactions of genomic elements are crucial for gene regulation.
- Chromosome Conformation Capture (3C) identifies these interactions by converting them into quantifiable ligation products.
- Existing 3C methods have limitations in throughput for large-scale analysis.
Purpose of the Study:
- To introduce a high-throughput 3C approach, 5C-Carbon Copy (5C), for comprehensive mapping of chromatin interactions.
- To apply 5C to analyze interaction networks within the human beta-globin locus and a gene desert region.
- To validate the efficacy of 5C in detecting known and novel looping interactions.
Main Methods:
- Developed 5C-Carbon Copy (5C), a high-throughput Chromosome Conformation Capture technique.
- Utilized microarrays and quantitative DNA sequencing (454-technology) for detection.
- Applied 5C to a 400-kb region of the human beta-globin locus and a 100-kb gene desert region.
Main Results:
- Successfully validated 5C by detecting previously identified looping interactions in the beta-globin locus.
- Discovered a novel looping interaction in K562 cells between the beta-globin Locus Control Region and the gamma-beta-globin intergenic region.
- Demonstrated 5C's capability for large-scale mapping of cis- and trans- interaction networks.
Conclusions:
- 5C-Carbon Copy (5C) is a powerful, high-throughput tool for mapping genome-wide chromatin interactions.
- The method facilitates the study of higher-order chromosome structure and its role in gene regulation.
- 5C provides new insights into regulatory mechanisms, such as developmental globin gene switching.
