Gene Regulatory Networks pp 211-225

Part of the Methods in Molecular Biology book series (MIMB, volume 786)

Detecting Long-Range Chromatin Interactions Using the Chromosome Conformation Capture Sequencing (4C-seq) Method

  • Nele Gheldof
  • Marion Leleu
  • Daan Noordermeer
  • Jacques Rougemont
  • Alexandre Reymond

Abstract

Eukaryotic transcription is tightly regulated by transcriptional regulatory elements, even though these elements may be located far away from their target genes. It is now widely recognized that these regulatory elements can be brought in close proximity through the formation of chromatin loops, and that these loops are crucial for transcriptional regulation of their target genes. The chromosome conformation capture (3C) technique presents a snapshot of long-range interactions, by fixing physically interacting elements with formaldehyde, digestion of the DNA, and ligation to obtain a library of unique ligation products. Recently, several large-scale modifications to the 3C technique have been presented. Here, we describe chromosome conformation capture sequencing (4C-seq), a high-throughput version of the 3C technique that combines the 3C-on-chip (4C) protocol with next-generation Illumina sequencing. The method is presented for use in mammalian cell lines, but can be adapted to use in mammalian tissues and any other eukaryotic genome.

Key words

Chromosome conformation capture Looping interactions Interactome Regulatory elements 

References

  1. 1.
    Dekker, J., Rippe, K., Dekker, M., and Kleckner, N. (2002) Capturing chromosome conformation. Science 295, 1306–1311.PubMedCrossRefGoogle Scholar
  2. 2.
    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. Proceedings of the National Academy of Sciences of the United States of America 103, 12463–12468.PubMedCrossRefGoogle Scholar
  3. 3.
    Tolhuis, B., Palstra, R. J., Splinter, E., Grosveld, F., and de Laat, W. (2002) Looping and interaction between hypersensitive sites in the active beta-globin locus. Molecular Cell 10, 1453–1465.PubMedCrossRefGoogle Scholar
  4. 4.
    Dostie, J., Richmond, T. A., Arnaout, R. A., Selzer, R. R., Lee, W. L., Honan, T. 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 Research 16, 1299–1309.PubMedCrossRefGoogle Scholar
  5. 5.
    Duan, Z., Andronescu, M., Schutz, K., McIlwain, S., Kim, Y. J., Lee, C., Shendure, J., Fields, S., Blau, C. A., and Noble, W. S. (2010) A three-dimensional model of the yeast genome. Nature 465, 363–367.PubMedCrossRefGoogle Scholar
  6. 6.
    Fullwood, M. J., Liu, M. H., Pan, Y. F., Liu, J., Xu, H., Mohamed, Y. B., Orlov, Y. L., Velkov, S., Ho, A., Mei, P. H., Chew, E. G. Y., Huang, P. Y. H., Welboren, W.-J., Han, Y., Ooi, H. S., Ariyaratne, P. N., Vega, V. B., Luo, Y., Tan, P. Y., Choy, P. Y., Wansa, K. D. S. A., Zhao, B., Lim, K. S., Leow, S. C., Yow, J. S., Joseph, R., Li, H., Desai, K. V., Thomsen, J. S., Lee, Y. K., Karuturi, R. K. M., Herve, T., Bourque, G., Stunnenberg, H. G., Ruan, X., Cacheux-Rataboul, V., Sung, W.-K., Liu, E. T., Wei, C.-L., Cheung, E., and Ruan, Y. (2009) An oestrogen-receptor-[agr]-bound human chromatin interactome. Nature 462, 58–64.PubMedCrossRefGoogle Scholar
  7. 7.
    Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., Sandstrom, R., Bernstein, B., Bender, M. A., Groudine, M., Gnirke, A., Stamatoyannopoulos, J., Mirny, L. A., Lander, E. S., and Dekker, J. (2009) Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science 326, 289–293.PubMedCrossRefGoogle Scholar
  8. 8.
    Schoenfelder, S., Sexton, T., Chakalova, L., Cope, N. F., Horton, A., Andrews, S., Kurukuti, S., Mitchell, J. A., Umlauf, D., Dimitrova, D. S., Eskiw, C. H., Luo, Y., Wei, C.-L., Ruan, Y., Bieker, J. J., and Fraser, P. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nature Genet. 42, 53–61.Google Scholar
  9. 9.
    Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B., and de Laat, W. (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nature Genet. 38, 1348–1354.PubMedCrossRefGoogle Scholar
  10. 10.
    Zhao, Z., Tavoosidana, G., Sjolinder, M., Gondor, A., Mariano, P., Wang, S., Kanduri, C., Lezcano, M., Sandhu, K. S., Singh, U., Pant, V., Tiwari, V., Kurukuti, S., and Ohlsson, R. (2006) Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nature Genet. 38, 1341–1347.PubMedCrossRefGoogle Scholar
  11. 11.
    Simonis, M., Kooren, J., and de Laat, W. (2007) An evaluation of 3C-based methods to capture DNA interactions. Nature Methods 4, 895–901.PubMedCrossRefGoogle Scholar
  12. 12.
    Miele, A., Gheldof, N., Tabuchi, T. M., Dostie, J., and Dekker, J. (2006) Mapping chromatin interactions by chromosome conformation capture. Current Protocols in Molecular Biology / edited by Frederick M. Ausubel et al. Chapter 21, Unit 21 11.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Nele Gheldof
    • 1
  • Marion Leleu
    • 2
  • Daan Noordermeer
    • 3
  • Jacques Rougemont
    • 4
  • Alexandre Reymond
    • 1
  1. 1.Center for Integrative GenomicsUniversity of Lausanne, Le Génopode, Quartier UNIL-SorgeLausanneSwitzerland
  2. 2.School of Life Sciences and Bioinformatics and Biostatistics Core FacilitySwiss Institute of Bioinformatics, Ecole Polytechnique Fédérale (EPFL)LausanneSwitzerland
  3. 3.School of Life SciencesEcole Polytechnique Fédérale (EPFL)LausanneSwitzerland
  4. 4.Bioinformatics and Biostatistics Core FacilitySwiss Institute of Bioinformatics, Ecole Polytechnique Fédérale (EPFL)LausanneSwitzerland

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