Abstract
To attempt to gain an understanding of the molecular underpinnings of disease, many researchers have turned to expression profiling of genes during various stages of host recognition, entry, invasive growth, and host responses. While these studies have proven valuable, a deeper level of knowledge of the control circuitry affecting observed gene expression profiles can lead to a better understanding of the host pathogen interaction. Transcription factors are key switches in signal transduction circuits regulating gene expression. One powerful method to define target sequence specificity for this important group of transcription regulators is chromatin immunoprecipitation (ChIP) with microarray chips (chip), commonly called ChIP-chip. A more recent variation of this technique is ChIP-seq where DNA sequencing replaces the microarray chip. Here, we describe how we elucidated the binding sites for the Magnaporthe oryzae Ca2+/calcineurin-dependent transcription factor MoCRZ1 with the ChIP-chip approach.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Bruno, K.S., Tenjo, F., Li, L., Hamer, J.E., and Xu, J.R. (2004) Cellular localization and role of kinase activity of PMK1 in Magnaporthe grisea. Eukaryot Cell. 3: 1525–32.
Dean, R.A. (1997) Siganl pathways and appressorium morphogenesis. Annual Rev. Phytopathology. 35: 211–234.
Dixon, K.P., Xu, J.R., Smirnoff, N., and Talbot, N.J. (1999) Independent signaling pathways regulate cellular turgor during hyperosmotic stress and appressorium-Âmediated plant infection by Magnaporthe Âgrisea. Plant Cell. 11: 2045–58.
Lee, S.C. and Lee, Y.H. (1998) Calcium/calmodulin-dependent signaling for appressorium formation in the plant pathogenic fungus Magnaporthe grisea. Mol Cells. 8: 698–704.
Mitchell, T.K. and Dean, R.A. (1995) The cAMP-dependent protein kinase catalytic Âsubunit is required for appressorium formation and pathogenesis by the rice blast pathogen Magnaporthe grisea. Plant Cell. 7: 1869–78.
Zelter, A., Bencina, M., Bowman, B.J., Yarden, O., and Read, N.D. (2004) A comparative genomic analysis of the calcium signaling machinery in Neurospora crassa, Magnaporthe grisea, and Saccharomyces cerevisiae. Fungal Genet Biol. 41: 827–41.
Ahn, I.P. and Suh, S.C. (2007) Calcium restores prepenetration morphogenesis abolished by methylglyoxal-bis-guanyl hydrazone in Cochliobolus miyabeanus infecting rice. Phytopathology. 97: 331–7.
Steinbach, W.J., Cramer, R.A., Jr., Perfect, B.Z., Asfaw, Y.G., Sauer, T.C., Najvar, L.K., Kirkpatrick, W.R., Patterson, T.F., Benjamin, D.K., Jr., Heitman, J., and Perfect, J.R. (2006) Calcineurin controls growth, morphology, and pathogenicity in Aspergillus fumigatus. Eukaryot Cell. 5: 1091–103.
Yang, Y., Cheng, P., Zhi, G., and Liu, Y. (2001) Identification of a calcium/calmodulin-Âdependent protein kinase that phosphorylates the Neurospora circadian clock protein FREQUENCY. J Biol Chem. 276: 41064–72.
Dean, R.A., Talbot, N.J., Ebbole, D.J., Farman, M.L., Mitchell, T.K., Orbach, M.J., Thon, M., Kulkarni, R., Xu, J.R., Pan, H., Read, N.D., Lee, Y.H., Carbone, I., Brown, D., Oh, Y.Y., Donofrio, N., Jeong, J.S., Soanes, D.M., Djonovic, S., Kolomiets, E., Rehmeyer, C., Li, W., Harding, M., Kim, S., Lebrun, M.H., Bohnert, H., Coughlan, S., Butler, J., Calvo, S., Ma, L.J., Nicol, R., Purcell, S., Nusbaum, C., Galagan, J.E., and Birren, B.W. (2005) The genome sequence of the rice blast fungus Magnaporthe grisea. Nature. 434: 980–6.
Mitchell, T.K., Thon, M., Jeong, J.S., Brown, D., Deng, J., and Dean, R.A. (2003) The rice blast pathosystem as a case study for the development of new tools and raw materials for genome analysis of fungal plant pathogens. New Phytologist. 159: 53–61.
Xu, J.R. and Xue, C. (2002) Time for a blast: genomics of Magnaporthe grisea. Mol Plant Pathol. 3: 173–176.
Talbot, N.J. (2003) On the trail of a cereal killer: Exploring the biology of Magnaporthe grisea. Annual Rev. Microbiol. 57: 177–202.
Choi, J., Kim, Y., Kim, S., Park, J., and Lee, Y.H. (2009) MoCRZ1, a gene encoding a calcineurin-responsive transcription factor, regulates fungal growth and pathogenicity of Magnaporthe oryzae. Fungal Genet Biol. 46: 243–54.
Buck, M.J. and Lieb, J.D. (2004) ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics. 83: 349–60.
Hanlon, S.E. and Lieb, J.D. (2004) Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays. Curr Opin Genet Dev. 14: 697–705.
Lieb, J.D., Liu, X., Botstein, D., and Brown, P.O. (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet. 28: 327–34.
Iyer, V.R., Horak, C.E., Scafe, C.S., Botstein, D., Snyder, M., and Brown, P.O. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 409: 533–8.
Mardis, E.R. (2007) ChIP-seq: welcome to the new frontier. Nat Methods. 4: 613–4.
Borneman, A.R., Gianoulis, T.A., Zhang, Z.D., Yu, H., Rozowsky, J., Seringhaus, M.R., Wang, L.Y., Gerstein, M., and Snyder, M. (2007) Divergence of transcription factor binding sites across related yeast species. Science. 317: 815–9.
Johnson, D.S., Li, W., Gordon, D.B., Bhattacharjee, A., Curry, B., Ghosh, J., Brizuela, L., Carroll, J.S., Brown, M., Flicek, P., Koch, C.M., Dunham, I., Bieda, M., Xu, X., Farnham, P.J., Kapranov, P., Nix, D.A., Gingeras, T.R., Zhang, X., Holster, H., Jiang, N., Green, R.D., Song, J.S., McCuine, S.A., Anton, E., Nguyen, L., Trinklein, N.D., Ye, Z., Ching, K., Hawkins, D., Ren, B., Scacheri, P.C., Rozowsky, J., Karpikov, A., Euskirchen, G., Weissman, S., Gerstein, M., Snyder, M., Yang, A., Moqtaderi, Z., Hirsch, H., Shulha, H.P., Fu, Y., Weng, Z., Struhl, K., Myers, R.M., Lieb, J.D., and Liu, X.S. (2008) Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 18: 393–403.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Kim, S., Mitchell, T.K. (2011). The Application of ChIP-chip Analysis in the Rice Blast Pathogen. In: Xu, JR., Bluhm, B. (eds) Fungal Genomics. Methods in Molecular Biology, vol 722. Humana Press. https://doi.org/10.1007/978-1-61779-040-9_8
Download citation
DOI: https://doi.org/10.1007/978-1-61779-040-9_8
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-039-3
Online ISBN: 978-1-61779-040-9
eBook Packages: Springer Protocols