Unit

UNIT 21.14 Chromosome Conformation Capture Carbon Copy Technology

  1. Josée Dostie1,2,
  2. Ye Zhan1,
  3. Job Dekker1

Published Online: 1 OCT 2007

DOI: 10.1002/0471142727.mb2114s80

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Dostie, J., Zhan, Y. and Dekker, J. 2007. Chromosome Conformation Capture Carbon Copy Technology. Current Protocols in Molecular Biology. 80:21.14:21.14.1–21.14.13.

Author Information

  1. 1

    University of Massachusetts Medical School, Worcester, Massachusetts

  2. 2

    McGill University, Montréal, Québec, Canada

Publication History

  1. Published Online: 1 OCT 2007
  2. Published Print: OCT 2007

Abstract

Chromosome conformation capture (3C) is used to quantify physical DNA contacts in vivo at high resolution. 3C was first used in yeast to map the spatial chromatin organization of chromosome III, and in higher eukaryotes to demonstrate that genomic DNA elements regulate target genes by physically interacting with them. 3C has been widely adopted for small-scale analysis of functional chromatin interactions along (cis) or between (trans) chromosomes. For larger-scale applications, chromosome conformation capture carbon copy (5C) combines 3C with ligation-mediated amplification (LMA) to simultaneously quantify hundreds of thousands of physical DNA contacts by microarray or ultra-high-throughput DNA sequencing. 5C allows the mapping of extensive networks of physical interactions among large sets of genomic elements throughout the genome. Such networks can provide important biological insights, e.g., by identifying relationships between regulatory elements and their target genes. This unit describes 5C for large-scale analysis of cis- and trans-chromatin interactions in mammalian cells. Curr. Protoc. Mol. Biol. 80:21.14.1-21.14.13. © 2007 by John Wiley & Sons, Inc.

Keywords:

  • chromatin structure;
  • epigenetic regulation;
  • genomics;
  • systems/network biology;
  • DNA looping;
  • transcription;
  • high throughput