Abstract
It is becoming increasingly apparent that chromatin is not randomly folded into the nucleus, but instead is highly organized into specific conformations within the nucleus. One consequence of such higher order structure is that chromatin looping can bring together genomic elements which are separated by several hundreds of kilobases, such as enhancers and promoters, and functionally facilitate their interaction. The Chromosome Conformation Capture (3C) assay is a powerful technique to detect looping structures and assess the probability of interaction between distant genomic elements (1–3). Here we describe the 3C methodology, its power, and limitations, together with the controls and normalization steps required for an accurate analysis.
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References
Splinter E, Grosveld F, de Laat W (2004) 3C technology: analyzing the spatial organization of genomic loci in vivo. Methods Enzymol 375:493–507
Dekker J (2006) The three ‘C’s of chromosome conformation capture: controls, controls, controls. Nat Methods 3:17–21
Miele A, Gheldof N, Tabuchi TM, Dostie J, Dekker J (2006) Mapping chromatin interactions by chromosome conformation capture. Curr Protoc Mol Biol Chapter 21, Unit 21.11
Chang HY, Cuvier O, Dekker J (2009) Gene dates, parties and galas. Symposium on Chromatin Dynamics and Higher Order Organization. EMBO Rep 10:689–693
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Nativio, R., Ito, Y., Murrell, A. (2012). Quantitative Chromosome Conformation Capture. In: Engel, N. (eds) Genomic Imprinting. Methods in Molecular Biology, vol 925. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-011-3_11
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DOI: https://doi.org/10.1007/978-1-62703-011-3_11
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Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-010-6
Online ISBN: 978-1-62703-011-3
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