Analysis of long-range chromatin interactions using Chromosome Conformation Capture

UMMS Affiliation

Program in Systems Biology; Program in Gene Function and Expression; Department of Biochemistry and Molecular Pharmacology

Publication Date


Document Type



Chromatin; Chromosomes; Nucleic Acid Conformation


Genetics and Genomics | Systems Biology


Chromosome Conformation Capture, or 3C, is a pioneering method for investigating the three-dimensional structure of chromatin. 3C is used to analyze long-range looping interactions between any pair of selected genomic loci. Most 3C studies focus on defined genomic regions of interest that can be up to several hundred Kb in size. The method has become widely adopted and has been modified to increase throughput to allow unbiased genome-wide analysis. These large-scale adaptations are presented in other articles in this issue of Methods. Here we describe the 3C procedure in detail, including the appropriate use of the technology, the experimental set-up, an optimized protocol and troubleshooting guide, and considerations for data analysis. The protocol described here contains previously unpublished improvements, which save time and reduce labor. We pay special attention to primer design, appropriate controls and data analysis. We include notes and discussion based on our extensive experience to help researchers understand the principles of 3C-based techniques and to avoid common pitfalls and mistakes. This paper represents a complete resource and detailed guide for anyone who desires to perform 3C.

DOI of Published Version



Methods. 2012 Nov;58(3):192-203. doi: 10.1016/j.ymeth.2012.07.022. Epub 2012 Aug 15. Link to article on publisher's site

Journal/Book/Conference Title

Methods (San Diego, Calif.)


Co-author Emily Smith is a doctoral student in the Interdisciplinary Graduate Program in the Graduate School of Biomedical Sciences (GSBS) at UMass Medical School.

Related Resources

Link to Article in PubMed

PubMed ID