Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

  1. Josée Dostie1,
  2. Todd A. Richmond2,
  3. Ramy A. Arnaout3,4,5,
  4. Rebecca R. Selzer2,
  5. William L. Lee3,
  6. Tracey A. Honan3,
  7. Eric D. Rubio6,
  8. Anton Krumm6,
  9. Justin Lamb3,
  10. Chad Nusbaum3,
  11. Roland D. Green2, and
  12. Job Dekker1,7
  1. 1Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605-0103, USA;
  2. 2NimbleGen Systems Inc., Madison, Wisconsin 53711, USA;
  3. 3Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141-2023, USA;
  4. 4Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115-6110, USA;
  5. 5Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts 02138-3758, USA;
  6. 6Department of Radiation Oncology, University of Washington School of Medicine, Seattle, Washington 98104, USA

    Abstract

    Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology. 3C converts physical chromatin interactions into specific ligation products, which are quantified individually by PCR. Here we present a high-throughput 3C approach, 3C-Carbon Copy (5C), that employs microarrays or quantitative DNA sequencing using 454-technology as detection methods. We applied 5C to analyze a 400-kb region containing the human β-globin locus and a 100-kb conserved gene desert region. We validated 5C by detection of several previously identified looping interactions in the β-globin locus. We also identified a new looping interaction in K562 cells between the β-globin Locus Control Region and the γ–β-globin intergenic region. Interestingly, this region has been implicated in the control of developmental globin gene switching. 5C should be widely applicable for large-scale mapping of cis- and trans- interaction networks of genomic elements and for the study of higher-order chromosome structure.

    Footnotes

    • ↵7 Corresponding author.

      ↵7 E-mail job.dekker{at}umassmed.edu; fax (508) 856-4650.

    • [Supplemental material is available online at www.genome.org.]

    • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.5571506.

      • Received June 2, 2006.
      • Accepted July 25, 2006.
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    1. Published in Advance September 5, 2006, doi: 10.1101/gr.5571506 Genome Res. 16: 1299-1309 Copyright © 2006, Cold Spring Harbor Laboratory Press

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