Nature Methods 3, 17 - 21 (2006)
Published online: 20 December 2005; | doi:10.1038/nmeth823
The three 'C' s of chromosome conformation capture: controls, controls, controlsJob Dekker
Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, Room 519, 364 Plantation Street, Worcester, Massachusetts 01605, USA.
Correspondence should be addressed to Job Dekker job.dekker@umassmed.edu 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 genes1,
2. 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) methodology3. 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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