Skip to main content
SpringerLink
Log in

Mapping In Vivo Protein–DNA Interactions in Plants by DamID, a DNA Adenine Methylation-Based Method

  • Protocol
  • First Online:
Plant Transcription Factors

Part of the book series: Methods in Molecular Biology ((MIMB,volume 754))

Abstract

DamID (DNA adenine methylation identification) is an adenine methylation-based tagging method designed to map protein–DNA interactions in vivo. DamID, an alternative method to chromatin immunoprecipitation (ChIP), is based on the covalent linking of a “fingerprint” in the vicinity of the DNA-binding sites of the protein of interest. The fingerprints can be further mapped by simple molecular approaches. First developed by van Steensel’s group in Drosophila melanogaster (1), DamID was successfully adapted to Arabidopsis thaliana, and its feasibility demonstrated by using the well-known yeast GAL4 transcription factor (2). The method was further used to establish a genome-wide map of the target sites of LHP1, a regulatory chromatin protein in A. thaliana (3).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. van Steensel, B., and Henikoff, S. (2000) Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat. Biotechnol. 18, 424–428.

    Article  PubMed  Google Scholar 

  2. Germann, S., Juul-Jensen, T., Letarnec, B., and Gaudin, V. (2006) DamID, a new tool for studying plant chromatin profiling in vivo, and its use to identify putative LHP1 target loci. Plant J. 48, 153–163.

    Article  PubMed  CAS  Google Scholar 

  3. Zhang, X., Germann, S., Blus, B. J., Khorasanizadeh, S., Gaudin, V., and Jacobsen, S. E. (2007) The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation. Nat. Struct. Mol. Biol. 14, 869–871.

    Article  PubMed  CAS  Google Scholar 

  4. van Steensel, B., and Henikoff, S. (2003) Epigenomic profiling using microarrays. Biotechniques 35, 346–350, 352–354, 356–357.

    PubMed  Google Scholar 

  5. Southall, T. D., and Brand, A. H. (2007) Chromatin profiling in model organisms. Brief Funct. Genomics Proteomics 6, 133–140.

    Article  CAS  Google Scholar 

  6. Moorman, C., Sun, L. V., Wang, J., de Wit, E., Talhout, W., Ward, L. D., Greil, F., Lu, X. J., White, K. P., Bussemaker, H. J., and van Steensel, B. (2006) Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 103, 12027–12032.

    Article  PubMed  CAS  Google Scholar 

  7. van Steensel, B., Delrow, J., and Henikoff, S. (2001) Chromatin profiling using targeted DNA adenine methyltransferase. Nat. Genet. 27, 304–308.

    Article  PubMed  Google Scholar 

  8. Sun, L. V., Chen, L., Greil, F., Negre, N., Li, T. R., Cavalli, G., Zhao, H., Van Steensel, B., and White, K. P. (2003) Protein–DNA interaction mapping using genomic tiling path microarrays in Drosophila. Proc. Natl. Acad. Sci. USA 100, 9428–9433.

    Article  PubMed  CAS  Google Scholar 

  9. Greil, F., van der Kraan, I., Delrow, J., Smothers, J. F., de Wit, E., Bussemaker, H. J., van Driel, R., Henikoff, S., and van Steensel, B. (2003) Distinct HP1 and Su(var)3–9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev. 17, 2825–2838.

    Article  PubMed  CAS  Google Scholar 

  10. de Wit, E., Greil, F., and van Steensel, B. (2007) High-resolution mapping reveals links of HP1 with active and inactive chromatin components. PLoS Genet. 3, e38.

    Article  PubMed  Google Scholar 

  11. Bianchi-Frias, D., Orian, A., Delrow, J. J., Vazquez, J., Rosales-Nieves, A. E., and Parkhurst, S. M. (2004) Hairy transcriptional repression targets and cofactor recruitment in Drosophila. PLoS Biol. 2, E178.

    Article  PubMed  Google Scholar 

  12. Orian, A., van Steensel, B., Delrow, J., Bussemaker, H. J., Li, L., Sawado, T., Williams, E., Loo, L. W., Cowley, S. M., Yost, C., Pierce, S., Edgar, B. A., Parkhurst, S. M., and Eisenman, R. N. (2003) Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network. Genes Dev. 17, 1101–1114.

    Article  PubMed  CAS  Google Scholar 

  13. Tolhuis, B., de Wit, E., Muijrers, I., Teunissen, H., Talhout, W., van Steensel, B., and van Lohuizen, M. (2006) Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster. Nat. Genet. 38, 694–699.

    Article  PubMed  CAS  Google Scholar 

  14. Pickersgill, H., Kalverda, B., de Wit, E., Talhout, W., Fornerod, M., and van Steensel, B. (2006) Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat. Genet. 38, 1005–1014.

    Article  PubMed  CAS  Google Scholar 

  15. Greil, F., de Wit, E., Bussemaker, H. J., and van Steensel, B. (2007) HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila. EMBO J. 26, 741–751.

    Article  PubMed  CAS  Google Scholar 

  16. Song, S., Cooperman, J., Letting, D. L., Blobel, G. A., and Choi, J. K. (2004) Identification of cyclin D3 as a direct target of E2A using DamID. Mol. Cell Biol. 24, 8790–8802.

    Article  PubMed  CAS  Google Scholar 

  17. Vogel, M. J., Guelen, L., de Wit, E., Peric-Hupkes, D., Loden, M., Talhout, W., Feenstra, M., Abbas, B., Classen, A. K., and van Steensel, B. (2006) Human heterochromatin proteins form large domains containing KRAB-ZNF genes. Genome Res. 16, 1493–1504.

    Article  PubMed  CAS  Google Scholar 

  18. Lebrun, E., Fourel, G., Defossez, P. A., and Gilson, E. (2003) A methyltransferase targeting assay reveals silencer–telomere interactions in budding yeast. Mol. Cell Biol. 23, 1498–1508.

    Article  PubMed  CAS  Google Scholar 

  19. Venkatasubrahmanyam, S., Hwang, W. W., Meneghini, M. D., Tong, A. H., and Madhani, H. D. (2007) Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A.Z. Proc. Natl. Acad. Sci. USA 104, 16609–16614.

    Article  PubMed  CAS  Google Scholar 

  20. Reddy, K. L., Zullo, J. M., Bertolino, E., and Singh, H. (2008) Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 452, 243–247.

    Article  PubMed  CAS  Google Scholar 

  21. Pindyurin, A. V., Moorman, C., de Wit, E., Belyakin, S. N., Belyaeva, E. S., Christophides, G. K., Kafatos, F. C., van Steensel, B., and Zhimulev, I. F. (2007) SUUR joins separate subsets of PcG, HP1 and B-type lamin targets in Drosophila. J. Cell. Sci. 120, 2344–2351.

    Article  PubMed  CAS  Google Scholar 

  22. Braunschweig, U., Hogan, G. J., Pagie, L., and van Steensel, B. (2009) Histone H1 binding is inhibited by histone variant H3.3. EMBO J. 28, 3635–3645.

    Article  PubMed  CAS  Google Scholar 

  23. Brooks, J. E., Blumenthal, R. M., and Gingeras, T. R. (1983) The isolation and characterization of the Escherichia coli DNA adenine methylase (dam) gene. Nucleic Acids Res. 11, 837–851.

    Article  PubMed  CAS  Google Scholar 

  24. Barras, F., and Marinus, M. G. (1989) The great GATC: DNA methylation in E. coli. Trends Genet. 5, 139–143.

    Article  PubMed  CAS  Google Scholar 

  25. Negre, N., Hennetin, J., Sun, L. V., Lavrov, S., Bellis, M., White, K. P., and Cavalli, G. (2006) Chromosomal distribution of PcG proteins during Drosophila development. PLoS Biol. 4, e170.

    Article  PubMed  Google Scholar 

  26. Fu, A. Q., and Adryan, B. (2009) Scoring overlapping and adjacent signals from genome-wide ChIP and DamID assays. Mol. Biosyst. 5, 1429–1438.

    Article  PubMed  CAS  Google Scholar 

  27. Caddick, M. X., Greenland, A. J., Jepson, I., Krause, K. P., Qu, N., Riddell, K. V., Salter, M. G., Schuch, W., Sonnewald, U., and Tomsett, A. B. (1998) An ethanol inducible gene switch for plants used to manipulate carbon metabolism. Nat. Biotechnol. 16, 177–180.

    Article  PubMed  CAS  Google Scholar 

  28. Koncz, C., and Schell, J. (1986) The promoter of the TL-DNA gene 5 controls the tissue-specific expression of chimeric genes carried by a novel type of Agrobacterium binary vector. Mol. Gen. Genet. 204, 383–396.

    Article  CAS  Google Scholar 

  29. Rozen, S., and Skaletsky, H. J. (2000) Primer3 on the WWW for general users and for biologist programmers. in “Bioinformatics Methods and Protocols: Methods in Molecular Biology” (Krawetz, S., and Misener, S., Eds.), pp. 365–386, Humana Press, Totowa, NJ.

    Google Scholar 

  30. van Blokland, R., Ross, S., Corrado, G., Scollan, C., and Meyer, P. (1998) Developmental abnormalities associated with deoxyadenosine methylation in transgenic tobacco. Plant J. 15, 543–551.

    Article  PubMed  Google Scholar 

  31. Roslan, H. A., Salter, M. G., Wood, C. D., White, M. R., Croft, K. P., Robson, F., Coupland, G., Doonan, J., Laufs, P., Tomsett, A. B., and Caddick, M. X. (2001) Characterization of the ethanol-inducible alc gene-expression system in Arabidopsis thaliana. Plant J. 28, 225–235.

    Article  PubMed  CAS  Google Scholar 

  32. Deveaux, Y., Peaucelle, A., Roberts, G. R., Coen, E., Simon, R., Mizukami, Y., Traas, J., Murray, J. A., Doonan, J. H., and Laufs, P. (2003) The ethanol switch: a tool for tissue-specific gene induction during plant development. Plant J. 36, 918–930.

    Article  PubMed  CAS  Google Scholar 

  33. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

    Google Scholar 

  34. Bechtold, N., Ellis, J., and Pelletier, G. (1993) In planta Agrobacterium mediated gene transfer by infiltration of adult Arabidopsis thaliana plants. C. R. Acad. Sci. Paris Life Sci. 316, 1194–1199.

    CAS  Google Scholar 

  35. Doyle, J. J., and Doyle, D. J. (1990) Isolation of plant DNA from fresh tissues. Focus 12, 13–15.

    Google Scholar 

  36. Vogel, M. J., Peric-Hupkes, D., and van Steensel, B. (2007) Detection of in vivo protein–DNA interactions using DamID in mammalian cells. Nat. Protoc. 2, 1467–1478.

    Article  PubMed  CAS  Google Scholar 

  37. Greil, F., Moorman, C., and van Steensel, B. (2006) DamID: mapping of in vivo protein–genome interactions using tethered DNA adenine methyltransferase. Methods Enzymol. 410, 342–359.

    Article  PubMed  CAS  Google Scholar 

  38. Orian, A., Abed, M., Kenyagin-Karsenti, D., and Boico, O. (2009) DamID: a methylation-based chromatin profiling approach. Methods Mol. Biol. 567, 155–169.

    Article  PubMed  Google Scholar 

  39. Urig, S., Gowher, H., Hermann, A., Beck, C., Fatemi, M., Humeny, A., and Jeltsch, A. (2002) The Escherichia coli dam DNA methyltransferase modifies DNA in a highly processive reaction. J. Mol. Biol. 319, 1085–1096.

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors thank Bas van Steensel for supplying the plasmids with the Dam coding sequence, as well as for his constant assistance, advice, and support for establishment of the DamID technique in plants. We thank Nicole Houba-Hérin and Mark Tepfer for critical reading of the manuscript.

Author information

Authors and Affiliations

  1. Institut National de la Santé et de la Recherche Médicale (Inserm), Centre Léon Bérard, Lyon Cedex, France

    Sophie Germann

  2. Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles Cedex, France

    Valérie Gaudin

Authors
  1. Sophie Germann
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Valérie Gaudin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Valérie Gaudin .

Editor information

Editors and Affiliations

  1. College of Agriculture, Dept. Plant & Soil Sciences, University of Kentucky, University Drive 1401, Lexington, 40546-0236, Kentucky, USA

    Ling Yuan

  2. Dept. Plant & Soil Sciences, University of Kentucky, Veterans Dr. 1405, Lexington, 40546-0312, Kentucky, USA

    Sharyn E. Perry

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Germann, S., Gaudin, V. (2011). Mapping In Vivo Protein–DNA Interactions in Plants by DamID, a DNA Adenine Methylation-Based Method. In: Yuan, L., Perry, S. (eds) Plant Transcription Factors. Methods in Molecular Biology, vol 754. Humana Press. https://doi.org/10.1007/978-1-61779-154-3_18

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-154-3_18

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-153-6

  • Online ISBN: 978-1-61779-154-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation