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The Nucleus pp 105-121 | Cite as

Mapping Cis- and Trans- Chromatin Interaction Networks Using Chromosome Conformation Capture (3C)

  • Adriana Miele
  • Job Dekker
Part of the Methods in Molecular Biology book series (MIMB, volume 464)

Abstract

Expression of genes can be controlled by regulatory elements that are located at large genomic distances from their target genes (in cis), or even on different chromosomes (in trans). Regulatory elements can act at large genomic distances by engaging in direct physical interactions with their target genes resulting in the formation of chromatin loops. Thus, genes and their regulatory elements come in close spatial proximity irrespective of their relative genomic positions. Analysis of interactions between genes and elements will reveal which elements regulate each gene, and will provide fundamental insights into the spatial organization of chromosomes in general.

Long-range cis- and trans- interactions can be studied at high resolution using chromosome conformation capture (3C) technology. 3C employs formaldehyde crosslinking to trap physical interactions between loci located throughout the genome. Crosslinked cells are solubilized and chromatin is digested with a restriction enzyme. Chromatin is subsequently ligated under conditions that favor intramolecular ligation. After reversal of the crosslinks, the DNA is purified and interaction frequencies between specific chromosomal loci are determined by quantifying the amounts of corresponding ligation products using polymerase chain reaction (PCR). This chapter describes detailed protocols for 3C analysis of chromatin interactions in the yeast Saccharomyces cerevisiae and in mammalian cells.

Keywords

DNA Chromatin looping Long-range gene regulation Trans- regulation Formaldehyde crosslinking Spatial organization 

Notes

Acknowledgments

Research in the Dekker laboratory is supported by grants from NIH (HG003143) and the Cystic Fibrosis Foundation.

References

  1. 1.
    Drissen, R., Palstra, R., Gillemano, N., Splinter, E., Grosveld, F., Philipsen, S., and de Laat, W. (2004) The active spatial organization of the β-globin locus requires the transcription factor EKLF. Genes Dev. 18, 2485-2490PubMedCrossRefGoogle Scholar
  2. 2.
    Vakoc, C., Letting, D.L., Gheldof, N., Sawado, T., Bender, M.A., Groudine, M., Weiss, M.J., Dekker, J., and Blobel, G.A. (2005) Proximity among distant regulatory elements at the betaglobin locus requires GATA-1 and FOG-1. Mol. Cell. 17, 453-462PubMedCrossRefGoogle Scholar
  3. 3.
    Dekker, J. (2002) Capturing chromosome conformation. Science. 295, 1306-1311PubMedCrossRefGoogle Scholar
  4. 4.
    Gheldof, N., Tabuchi, T.M., and Dekker, J. (2006) The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications. Proc. Natl. Acad. Sci. USA. 103, 12463-12468PubMedCrossRefGoogle Scholar
  5. 5.
    Tolhuis, B., Palstra, R.J., Splinter, E., Grosveld, F., and de Laat, W. (2002) Looping interaction between hypersensitive sites in the active beta-globin locus. Mol. Cell. 10, 1435-1465CrossRefGoogle Scholar
  6. 6.
    Palstra, R.J., Tolhuis, B., Splinter, E., Nijmeijer, R., Grosveld, F., and de Laat, W. (2003) The ?-globin nuclear compartment in development and erythroid differentiation. Nat. Genet. 25, 190-194CrossRefGoogle Scholar
  7. 7.
    Dostie, J., Richmond, R.A., Arnaout, R.A., Selzer, R.R., Lee, W.L., Honan, A., Rubio, E.D., Krumm, A., Lamb, J., Nusbaum, C., Green, R.D., and Dekker, J. (2006) Chromosome conformation capture carbon copy (5C): A massively parallel solution for mapping interactions between genomic elements. Genome Res. 16, 1299-1309PubMedCrossRefGoogle Scholar
  8. 8.
    Liu, Z., and Garrard, W.T. (2005) Long-range interactions between three transcriptional enhancers, active Vkappa gene promoters, and a 3? boundary sequence spanning 46 kilobases. Mol. Cell. Biol. 25, 3220-3231PubMedCrossRefGoogle Scholar
  9. 9.
    Murrell, A., Heeson, S., and Reik, W. (2004) Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat. Genet. 36, 889-893PubMedCrossRefGoogle Scholar
  10. 10.
    Spilianakis, C.G., Lalioti, M.D., Town, T., Lee, G.R., and Flavell, R.A. (2005) Interchromosomal associations between alternatively expressed loci. Nature. 435, 637-645PubMedCrossRefGoogle Scholar
  11. 11.
    Lomvardas, S., Barnea, G., Pisapia, D.J., Mendelsohn, M., Kirkland, J., and Axel, R. (2006) Interchromosomal interactions and olfactory receptor choice. Cell. 126, 403-413PubMedCrossRefGoogle Scholar
  12. 12.
    Dekker, J. (2006) The three C’s of chromosome conformation capture: controls, controls, controls. nat. methods. 3, 17-21PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science + Business Media, LLC 2008

Authors and Affiliations

  • Adriana Miele
    • 1
  • Job Dekker
    • 1
  1. 1.Program in Gene Function and Expression and Department of Biochemistry and Molecular PharmacologyUniversity of Massachusetts Medical SchoolWorcesterUSA

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