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Gene-Specific and Genome-Wide ChIP Approaches to Study Plant Transcriptional Networks

  • Dmitry A. Belostotsky
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 553)

Keywords

Whole Genome Amplification Tiling Array ChIP Experiment Disuccinimidyl Suberate Dimethyl Suberimidate 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

We thank Herbert Auer for helping us develop the ChIP-chip method for Arabidopsis and for comments on this manuscript, Manli Davis for helping us grow and collect plant materials, and Marko Djordjevic for assistance with the analysis of ChIP-chip data. This research was supported by National Science Foundation (NSF) grant MCB-0418891 and by NRI grant 2007-35318-17805 from the USDA-CSREES to E.G.

References

  1. 1.
    Grotewold, E. and Springer, N. (2009) Decoding the transcriptional hardwiring of the plant genome. In: Coruzzi, G. and Gutierrez, R. (eds). In Systems Biology. Blackwell Publishing. In Press.Google Scholar
  2. 2.
    Sablowski, R.W. and Meyerowitz, E.M. (1998) A homolog of NO APICAL MERISTEM is an immediate target of the floral homeotic genes APETALA3/PISTILLATA. Cell. 92, 93–103.PubMedCrossRefGoogle Scholar
  3. 3.
    Spelt, C., Quattrocchio, F., Mol, J., and Koes, R. (2002) ANTHOCYANIN1 of petunia controls pigment synthesis, vacuolar pH, and seed coat development by genetically distinct mechanisms. Plant Cell. 14, 2121–2135.PubMedCrossRefGoogle Scholar
  4. 4.
    Shin, B., Choi, G., Yi, H., et al. (2002) AtMYB21, a gene encoding a flower-specific transcription factor, is regulated by COP1. Plant J. 30, 23–32.PubMedCrossRefGoogle Scholar
  5. 5.
    Wang, D., Amornsiripanitch, N., and Dong, X. (2006) A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathog. 2, e123.PubMedCrossRefGoogle Scholar
  6. 6.
    Wellmer, F., Alves-Ferreira, M., Dubois, A., Riechmann, J.L., and Meyerowitz, E.M. (2006) Genome-wide analysis of gene expression during early Arabidopsis flower development. PLoS Genet. 2, e117.PubMedCrossRefGoogle Scholar
  7. 7.
    Wells, J. and Farnham, P.J. (2002) Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods. 26, 48–56.PubMedCrossRefGoogle Scholar
  8. 8.
    Nowack, D.E., Tian, B., and Brasier, A.R. (2005) Two-step cross-linking method for identification of NF-KB gene network by chromatin immunoprecipitation. Biotechniques. 39, 715–725.CrossRefGoogle Scholar
  9. 9.
    Buck, M.J., Nobel, A.B., and Lieb, J.D. (2005) ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biol. 6, R97.PubMedCrossRefGoogle Scholar
  10. 10.
    Thibaud-Nissen, F., Wu, H., Richmond, T., et al. (2006) Development of Arabidopsis whole-genome microarrays and their application to the discovery of binding sites for the TGA2 transcription factor in salicylic acid-treated plants. Plant J. 47, 152–162.PubMedCrossRefGoogle Scholar
  11. 11.
    Lee, J., He, K., Stolc, V., et al. (2007) Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell. 19, 731–749.PubMedCrossRefGoogle Scholar
  12. 12.
    Zhang, X., Clarenz, O., Cokus, S., et al. (2007) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 5, e129.PubMedCrossRefGoogle Scholar
  13. 13.
    Zhang, X., Yazaki, J., Sundaresan, A., et al. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell. 126, 1189–1201.PubMedCrossRefGoogle Scholar
  14. 14.
    O'Geen, H., Nicolet, C.M., Blahnik, K., Green, R., and Farnham, P.J. (2006) Comparison of sample preparation methods for ChIP-chip assays. Biotechniques. 41, 577–580.PubMedCrossRefGoogle Scholar
  15. 15.
    Johnson, W.E., Li, W., Meyer, C.A., et al. (2006) Model-based analysis of tiling-arrays for ChIP-chip. Proc. Natl. Acad. Sci. USA. 103, 12457–12462.Google Scholar
  16. 16.
    Wei, C.L., Wu, Q., Vega, V.B., et al. (2006) A global map of p53 transcription-factor binding sites in the human genome. Cell. 124, 207–219.PubMedCrossRefGoogle Scholar
  17. 17.
    Denissov, S., van Driel, M., Voit, R., et al. (2007) Identification of novel functional TBP-binding sites and general factor repertoires. EMBO J. 26, 944–954.PubMedCrossRefGoogle Scholar
  18. 18.
    Hermanson, G.T. (1996) Bioconjugate Techniques. San Diego: Academic Press.Google Scholar
  19. 19.
    Morohashi, K. and Grotewold, E. (2009) A systems approach reveals regulatory circuitry for Arabidopsis trichome initiation by the GL3 and GL1 selectors. PLoS Genetics. 5, e1000396Google Scholar
  20. 20.
    Xie, Z. and Grotewold, E. (2008) Serial ChIP as a tool to investigate the co-localization or exclusion of proteins on plant genes. Plant Methods. 4, 25.Google Scholar
  21. 21.
    Morohashi, K., Zhao, M., Yang, M., Read, B., Lloyd, A., Lamb, R., and Grotewold, E. (2007) Participation of the Arabidopsis bHLH factor GL3 in trichome initiation regulatory events. Plant Physiol. 145, 736–746.Google Scholar

Copyright information

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

Authors and Affiliations

  • Dmitry A. Belostotsky

There are no affiliations available

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