Hox Genes pp 279-289 | Cite as

DamID as an Approach to Studying Long-Distance Chromatin Interactions

  • Fabienne Cléard
  • François Karch
  • Robert K. MaedaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1196)


How transcription is controlled by distally located cis-regulatory elements is an active area of research in biology. As such, there have been many techniques developed to probe these long-distance chromatin interactions. Here, we focus on one such method, called DamID (van Steensel and Henikoff, Nat Biotechnol 18(4):424–428, 2000). While other methods like 3C (Dekker et al., Science 295(5558):1306–1311, 2002), 4C (Simonis et al., Nat Genet 38(11):1348–1354, 2006; Zhao et al., Nat Genet 38(11):1341–1347, 2006), and 5C (Dostie et al., Genome Res 16(10):1299–1309, 2006) are undoubtedly powerful, the DamID method can offer some advantages over these methods if the genetic locus can be easily modified. The lack of tissue fixation, the low amounts of starting material required to perform the experiment, and the relatively modest hardware requirements make DamID experiments an interesting alternative to consider when examining long-distance chromatin interactions.

Key words

Dam methyltransferase DamID Drosophila Chromatin Long-distance interactions Gene regulation 


  1. 1.
    van Steensel B, Henikoff S (2000) Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18(4):424–428. doi: 10.1038/74487 PubMedCrossRefGoogle Scholar
  2. 2.
    van Steensel B, Delrow J, Henikoff S (2001) Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet 27(3):304–308. doi: 10.1038/85871 PubMedCrossRefGoogle Scholar
  3. 3.
    Cleard F, Moshkin Y, Karch F, Maeda RK (2006) Probing long-distance regulatory interactions in the Drosophila melanogaster bithorax complex using Dam identification. Nat Genet 38(8):931–935PubMedCrossRefGoogle Scholar
  4. 4.
    Maeda RK, Karch F (2006) The ABC of the BX-C: the bithorax complex explained. Development 133(8):1413–1422PubMedCrossRefGoogle Scholar
  5. 5.
    Maeda RK, Karch F (2007) Making connections: boundaries and insulators in Drosophila. Curr Opin Genet Dev 17(5):394–399. doi: 10.1016/j.gde.2007.08.002 PubMedCrossRefGoogle Scholar
  6. 6.
    Muravyova E, Golovnin A, Gracheva E, Parshikov A, Belenkaya T, Pirrotta VV, Georgiev P (2001) Loss of insulator activity by paired Su(Hw) chromatin insulators. Science 291(5503):495–498PubMedCrossRefGoogle Scholar
  7. 7.
    Cai HN, Shen P (2001) Effects of cis arrangement of chromatin insulators on enhancer-blocking activity. Science 291(5503):493–495PubMedCrossRefGoogle Scholar
  8. 8.
    Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295(5558):1306–1311. doi:10.1126/science.1067799PubMedCrossRefGoogle Scholar
  9. 9.
    Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38(11):1348–1354. doi: 10.1038/ng1896 PubMedCrossRefGoogle Scholar
  10. 10.
    Zhao Z, Tavoosidana G, Sjolinder M, Gondor A, Mariano P, Wang S, Kanduri C, Lezcano M, Sandhu KS, Singh U, Pant V, Tiwari V, Kurukuti S, Ohlsson R (2006) Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet 38(11):1341–1347. doi: 10.1038/ng1891 PubMedCrossRefGoogle Scholar
  11. 11.
    Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C, Green RD, Dekker J (2006) Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 16(10):1299–1309. doi: 10.1101/gr.5571506 PubMedCentralPubMedCrossRefGoogle Scholar
  12. 12.
    Fullwood MJ, Ruan Y (2009) ChIP-based methods for the identification of long-range chromatin interactions. J Cell Biochem 107(1):30–39. doi: 10.1002/jcb.22116 PubMedCentralPubMedCrossRefGoogle Scholar
  13. 13.
    Southall TD, Gold KS, Egger B, Davidson CM, Caygill EE, Marshall OJ, Brand AH (2013) Cell-type-specific profiling of gene expression and chromatin binding without cell isolation: assaying RNA Pol II occupancy in neural stem cells. Dev Cell. doi: 10.1016/j.devcel.2013.05.020 PubMedCentralGoogle Scholar
  14. 14.
    Applied_Biosystems (2004) Guide to performing relative quantitation of gene expression using real-time quantitative PCR.Google Scholar
  15. 15.
    Rohlf FJ, Sokal RR, Sokal RR (1981) Statistical tables, 2nd edn. Freeman, San Francisco, CAGoogle Scholar
  16. 16.
    Scheffé H (1961) The analysis of variance. Wiley, New York, NYGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Fabienne Cléard
    • 1
  • François Karch
    • 1
  • Robert K. Maeda
    • 1
    Email author
  1. 1.Department of Genetics and EvolutionUniversity of GenevaGeneva-4Switzerland

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