A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes

Methods. 2012 Nov;58(3):277-88. doi: 10.1016/j.ymeth.2012.06.018. Epub 2012 Jul 6.


Accumulating evidence demonstrates that the three-dimensional (3D) organization of chromosomes within the eukaryotic nucleus reflects and influences genomic activities, including transcription, DNA replication, recombination and DNA repair. In order to uncover structure-function relationships, it is necessary first to understand the principles underlying the folding and the 3D arrangement of chromosomes. Chromosome conformation capture (3C) provides a powerful tool for detecting interactions within and between chromosomes. A high throughput derivative of 3C, chromosome conformation capture on chip (4C), executes a genome-wide interrogation of interaction partners for a given locus. We recently developed a new method, a derivative of 3C and 4C, which, similar to Hi-C, is capable of comprehensively identifying long-range chromosome interactions throughout a genome in an unbiased fashion. Hence, our method can be applied to decipher the 3D architectures of genomes. Here, we provide a detailed protocol for this method.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Biotinylation
  • Chromosome Mapping / methods*
  • Cross-Linking Reagents / chemistry
  • DNA Cleavage
  • DNA Restriction Enzymes / chemistry
  • DNA, Circular / chemistry
  • DNA, Circular / genetics
  • DNA, Circular / isolation & purification
  • DNA, Fungal / chemistry
  • DNA, Fungal / genetics
  • Formaldehyde / chemistry
  • Gene Library
  • Genome, Fungal*
  • Humans
  • Nucleic Acid Conformation
  • ROC Curve
  • Saccharomyces cerevisiae / genetics*
  • Sequence Analysis, DNA


  • Cross-Linking Reagents
  • DNA, Circular
  • DNA, Fungal
  • Formaldehyde
  • DNA Restriction Enzymes