Summary
Disruption of epigenetic regulators of transcription is a central mechanism of oncogenesis. Many of the advances in the understanding of these mechanisms are attributable to the successful development of chromatin immunoprecipitation (ChIP) for in vivo detection of histone modifications as well as chromatin binding regulatory proteins. This is a powerful technique for analyzing histone modifications as well as binding sites for proteins that bind either directly or indirectly to DNA. Here we present two ChIP protocols. The first is particularly useful for identifying histone modifications or binding at specific, known genomic sites. The second, employing serial analysis of gene expression, is particularly powerful for the discovery of previously unidentified sites of modification or binding.
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References
Orlando, V. (2000). Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem Sci 25:99–104.
Kirmizis, A. and Farnham, P.J. (2004). Genomic approaches that aid in the identification of transcription factor target genes. Exp Biol Med 229:705–721.
Huebert, D.J., Kamal, M., O’Donovan, A., and Bernstein, B.E. (2006). Genome-wide analysis of histone modifications by ChIP on chip. Methods 40:365–369.
Shivaswamy, S. and Iyer, V.R. (2007). Genome analysis of chromatin status using tiling microarrays. Methods 41:304–311.
Robyr, D., Kurdistani, S.K. and Grunstein, M. (2004). Analysis of genome-wide histone acetylation state and enzyme binding using DNA microarrays. Methods Enzymol 376:289–304.
Saha, S., Sparks, A.B., Rago, C., Akmaev, V., Wang, C.J., Vogelstein, B., Kinzler, K.W. and Velculsecu, V.E. (2002). Using the transcriptome to annotate the genome. Nat Biotechnol 20:508–512.
Roh, T.Y., Ngau, W.C., Cui, K., Landsman, D. and Zhao, K. (2004). High-resolution genome-wide mapping of histone modifications. Nat Biotechnol 22:1013–1016.
Roh, T.Y., Cuddapah, S. and Zhao, K. (2005). Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev 19:542–552.
Roh, T.Y., Cuddapah, S., Cui, K., and Zhao, K. (2006). The genomic landscape of histone modifications in human T cells. Proc Natl Acad Sci 103:15782–15787.
Milne A. et al. (2005). Leukemogenic MLL fusion proteins bind across a broad region of the Hoxa9 locus, promoting transcription and multiple histone modifications. Cancer Res 65:11367–11374.
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© 2009 Humana Press, a part of Springer Science+Business Media, LLC
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Milne, T.A., Zhao, K., Hess, J.L. (2009). Chromatin Immunoprecipitation (ChIP) for Analysis of Histone Modifications and Chromatin-Associated Proteins. In: Eric So, C.W. (eds) Leukemia. Methods in Molecular Biology™, vol 538. Humana Press. https://doi.org/10.1007/978-1-59745-418-6_21
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DOI: https://doi.org/10.1007/978-1-59745-418-6_21
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