Chromatin Charting: Global Mapping of Epigenetic Effects

  • Chongyuan Luo
  • Eric Lam
Part of the Methods in Molecular Biology™ book series (MIMB, volume 553)


To tackle the question of how chromatin organization is involved in global regulation of genome-related processes such as transcription, we have recently created a collection of 277 transposon-tagged Arabidopsis lines comprised of a single insert with a common luciferase reporter cassette and a LacO repeat array for visual tracking of the tagged region via fluorescent protein fusion technology. Using this collection of plants, one can begin to map transgene position effects as well as global epigenetic control in response to developmental or externally applied cues. In this chapter, we will outline the approach and methods for deploying this novel resource for the study of global gene control, using Arabidopsis as a convenient model system.

Key words

Chromatin transposon-tagged lines Arabidopsis epigenetics luciferase dsRNA suppression position effects 



This work is supported by an NSF Plant Genome Research Program grant to E.L. (#0077617).


  1. 1.
    Brink, R.A. (1956) A genetic change associated with the R locus in maize which is directed and potentially reversible. Genetics 41, 872–889.PubMedGoogle Scholar
  2. 2.
    Chandler, V. and Stam, M. (2004) Chromatin conversations: mechanisms and implications of paramutation. Nat. Rev. Genet. 5, 532–544.PubMedCrossRefGoogle Scholar
  3. 3.
    Grummt, I. and Pikaard, C.S. (2003) Epigenetic silencing of RNA polymerase I transcription. Nat. Rev. Mol. Cell Biol. 4, 641–649.PubMedCrossRefGoogle Scholar
  4. 4.
    Matzke, M.A. and Birchler, J.A. (2005) RNAi-mediated pathways in the nucleus. Nat. Rev. Genet. 6, 24–35.PubMedCrossRefGoogle Scholar
  5. 5.
    Wolffe, A.P. and Matzke, M.A. (1999) Epigenetics: regulation through repression. Science 286, 481–486.PubMedCrossRefGoogle Scholar
  6. 6.
    Hsieh, T.-F. and Fischer, R.L. (2005) Biology of chromatin dynamics. Annu. Rev. Plant Biol. 56, 327–351.PubMedCrossRefGoogle Scholar
  7. 7.
    Reyes, J.C. (2006) Chromatin modifiers that control plant development. Curr. Opin. Plant Biol. 9, 21–27.PubMedCrossRefGoogle Scholar
  8. 8.
    Bender, J. (2004) DNA methylation and epigenetics. Annu. Rev. Plant Biol. 55, 41–68.PubMedCrossRefGoogle Scholar
  9. 9.
    Chan, S.W.-L., Henderson, I.R., and Jacobsen, S.E. (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev. Genet. 6, 351–360.PubMedCrossRefGoogle Scholar
  10. 10.
    Fuchs, J., Demidov, D., Houben, A., and Schubert, I. (2006) Chromosomal histone modification patterns – from conservation to diversity. Trends Plant Sci. 11, 199–208.PubMedCrossRefGoogle Scholar
  11. 11.
    Barrera, L.O. and Ren, B. (2006) The transcriptional regulatory code of eukaryotic cells – insights from genome-wide analysis of chromatin organization and transcription factor binding. Curr. Opin. Cell Biol. 18, 291–298.PubMedCrossRefGoogle Scholar
  12. 12.
    He, Y. and Amasino, R.M. (2004) Role of chromatin modification in flowering-time control. Trends Plant Sci. 10, 30–35.CrossRefGoogle Scholar
  13. 13.
    Lippman, Z. and Martienssen, R. (2004) The role of RNA interference in heterochromatic silencing. Nature 431, 364–370.PubMedCrossRefGoogle Scholar
  14. 14.
    Pontes, O., Li, C.F., Nunes, P.C., Haag, J., Ream, T., Vitins, A., Jacobsen, S.E., and Pikaard, C.S. (2006) The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell 126, 79–92.PubMedCrossRefGoogle Scholar
  15. 15.
    Alleman, M., Sidorenko, L., McGinnis, K., Seshadri, V., Dorweiler, J.E., White, J., Sikkink, K., and Chandler, V.L. (2006) An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 442, 295–298.PubMedCrossRefGoogle Scholar
  16. 16.
    McGinnis, K.M., Springer, C., Lin, Y., Carey, C.C., and Chandler, V. (2006) Transcriptionally silenced transgenes in maize are activated by three mutations defective in paramutation. Genetics 173, 1637–1647.PubMedCrossRefGoogle Scholar
  17. 17.
    Elmayan, T., Proux, F., and Vaucheret, H. (2005) Arabidopsis RPA2: a genetic link among transcriptional gene silencing, DNA repair, and DNA replication. Curr. Biol. 15, 1919–1925.PubMedCrossRefGoogle Scholar
  18. 18.
    Lippman, Z., et al. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430, 471–476.PubMedCrossRefGoogle Scholar
  19. 19.
    Probst, A.V., Fransz, P.F., Paszkowski, J., and Mittelsten-Scheid, O. (2003) Two means of transcriptional reactivation within heterochromatin. Plant J. 33, 743–749.PubMedCrossRefGoogle Scholar
  20. 20.
    Cremer, T., Cremer, M., Dietzel, S., Muller, S., Solovei, I., and Fakan, S. (2006) Chromosome territories – a functional nuclear landscape. Curr. Opin. Cell Biol. 18, 307–316.PubMedCrossRefGoogle Scholar
  21. 21.
    Kosak, S.T. and Groudine, M. (2004) Gene order and dynamic domains. Science 306, 644–647.PubMedCrossRefGoogle Scholar
  22. 22.
    Sundaresan, V., Springer, P., Volpe, T., Howard, S., Jones, J.D.G., Dean, C., Ma, H., and Martienssen, R. (1995) Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. Genes Dev. 9, 1797–1810.PubMedCrossRefGoogle Scholar
  23. 23.
    Kato, N. and Lam, E. (2001) Detection of chromosomes tagged with green fluorescent protein in live Arabidopsis thaliana plants. Genome Biol. 2, research 0045.1–0045.10.CrossRefGoogle Scholar
  24. 24.
    Rosin, R., Watanabe, N., Cacas, J.-L., Kato, N., Arroyo, J.M., Fang, Y., May, B., Vaughn, M., Simorowski, J., Ramu, U., McCombie, R.W., Spector, D.L., Martienssen, R.A., and Lam, E. (2008) Genome-wide transposon tagging reveals location-dependent effects on transcription and chromatin organization in Arabidopsis. Plant J. 55(3): 514–525.Google Scholar
  25. 25.
    Kato, N. and Lam, E. (2003) Chromatin of endoreduplicated pavement cells has greater range of movement than that of diploid guard cells in Arabidopsis thaliana. J. Cell Sci. 116, 2195–2201.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Chongyuan Luo
    • 1
  • Eric Lam
    • 1
  1. 1.Biotechnology Center for Agriculture and the EnvironmentRutgers UniversityNew BrunswickUSA

Personalised recommendations