The three 'C' s of chromosome conformation capture: controls, controls, controls

UMMS Affiliation

Program in Gene Function and Expression



Document Type


Medical Subject Headings

Chromosomes; DNA; Gene Expression Regulation; Genes; Genomics; Nucleic Acid Conformation; Polymerase Chain Reaction; *Regulatory Elements, Transcriptional; Reproducibility of Results


Genetics and Genomics


Transcription regulation in higher eukaryotes is controlled by regulatory elements such as enhancers that are recognized by transcription factors. In many cases regulatory elements can be located at distances up to several megabases from their target genes. Recent evidence shows that long-range control of gene expression can be mediated through direct physical interactions between genes and these regulatory elements. Such looping interactions can be detected using the chromosome conformation capture (3C) methodology. Although 3C is experimentally straightforward, to draw meaningful conclusions one must carefully design 3C experiments and implement the conscientious use of controls. The general guidelines presented here should help experimental design and minimize misinterpretation of 3C experiments.

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Citation: Nat Methods. 2006 Jan;3(1):17-21. Link to article on publisher's site

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