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An evaluation of 3C-based methods to capture DNA interactions

Nature Methods volume 4, pages 895–901 (2007)Cite this article

Abstract

The shape of the genome is thought to play an important part in the coordination of transcription and other DNA-metabolic processes. Chromosome conformation capture (3C) technology allows us to analyze the folding of chromatin in the native cellular state at a resolution beyond that provided by current microscopy techniques. It has been used, for example, to demonstrate that regulatory DNA elements communicate with distant target genes through direct physical interactions that loop out the intervening chromatin fiber. Here we discuss the intricacies of 3C and new 3C-based methods including the 4C, 5C and ChIP-loop assay.

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Figure 1: Schematic representation of 3C-based methods.
Figure 2: Ligation events measured at the β-globin locus.
Figure 3: Outline of the two basic 4C strategies.
Figure 4: Results obtained by 4C technology are highly reproducible.

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Acknowledgements

We thank F. Grosveld and the members of our laboratory for discussion. This work was supported by grants from the Dutch Scientific Organization (NWO) (016-006-026) and (912-04-082) to W.d.L.

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Author notes

  1. Marieke Simonis and Jurgen Kooren: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Cell Biology and Genetics, Erasmus MC, PO Box 2040, Rotterdam, 3000 CA, The Netherlands

    Marieke Simonis, Jurgen Kooren & Wouter de Laat

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  1. Marieke Simonis
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  2. Jurgen Kooren
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  3. Wouter de Laat
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Correspondence to Wouter de Laat.

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Competing interests

W.d.L. holds a patent application no. PCT/IB2006/002268 on 4C technology.

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Simonis, M., Kooren, J. & de Laat, W. An evaluation of 3C-based methods to capture DNA interactions. Nat Methods 4, 895–901 (2007). https://doi.org/10.1038/nmeth1114

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