Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation

Methods. 2012 Nov;58(3):221-30. doi: 10.1016/j.ymeth.2012.04.009. Epub 2012 May 17.


Chromosome Conformation Capture (3C) and 3C-based technologies are constantly evolving in order to probe nuclear organization with higher depth and resolution. One such method is 4C-technology that allows the investigation of the nuclear environment of a locus of choice. The use of Illumina next generation sequencing as a detection platform for the analysis of 4C data has further improved the sensitivity and resolution of this method. Here we provide a step-by-step protocol for 4C-seq, describing the procedure from the initial template preparation until the final data analysis, interchanged with background information and considerations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Cells, Cultured
  • Chromatin / chemistry
  • Chromatin / genetics
  • Chromosome Mapping / methods*
  • DNA / chemistry
  • DNA / genetics
  • DNA / isolation & purification
  • DNA Cleavage
  • DNA Ligases / chemistry
  • DNA Primers / genetics
  • DNA Restriction Enzymes / chemistry
  • Data Interpretation, Statistical
  • Epistasis, Genetic
  • Female
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Sequence Analysis, DNA*
  • Tissue Fixation / methods


  • Chromatin
  • DNA Primers
  • DNA
  • DNA Restriction Enzymes
  • DNA Ligases