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Related Experiment Videos

Mapping networks of physical interactions between genomic elements using 5C technology.

Josée Dostie1, Job Dekker

  • 1Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, 364 Plantation Street, Room 519, Worcester, Massachusetts 01605-4321, USA.

Nature Protocols
|April 21, 2007
PubMed
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Chromosome conformation capture (5C) technology measures millions of chromatin interactions. This high-throughput method, based on chromosome conformation capture (3C), enables parallel analysis of gene regulation and chromosomal processes.

Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Genomic elements interact over large distances to regulate genes.
  • Chromosome conformation capture (3C) detects these interactions.
  • A high-throughput adaptation of 3C, called 5C, is needed for large-scale analysis.

Purpose of the Study:

  • To describe the 5C technology for measuring chromatin interactions.
  • To enable parallel analysis of millions of chromatin interactions.
  • To provide a detailed protocol for the 5C method.

Main Methods:

  • Cells are cross-linked with formaldehyde.
  • Chromatin is digested, ligated at low DNA concentration, and purified.
  • 5C uses multiplexed ligation-mediated amplification (LMA) for detection and analysis via microarray or sequencing.

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Main Results:

  • The 5C protocol allows for high-throughput measurement of chromatin interaction networks.
  • This method can analyze millions of interactions in parallel.
  • The complete 5C protocol can be finished within 13 days.

Conclusions:

  • 5C is a powerful tool for studying long-range gene regulation.
  • The technology facilitates comprehensive analysis of 3D genome organization.
  • 5C offers a scalable and efficient approach to mapping chromatin interactions.