Abstract
Chromatin immunoprecipitation (ChIP) is an invaluable method to study the specific interaction of regulatory proteins with genomic DNA. Since its first development, it has been modified extensively to make it applicable to many different cell types and experimental systems. The cross-linking of regulatory proteins to genomic DNA requires monolayer cells or single cell suspensions. Here, we describe a ChIP protocol using embryoid bodies formed at the early stage differentiation of pluripotent stem cells, which we have used to determine long-range p300-dependent regulatory elements of myogenic-specific genes.
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Orlando V (2000) Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem Sci 25:99–104
O’Neill LP, Turner BM (1995) Histone H4 acetylation distinguishes coding regions of the human genome from heterochromatin in a differentiation-dependent but transcription-independent manner. EMBO J 14:3946–3957
O’Neill LP, Turner BM (1996) Immunoprecipitation of chromatin. Methods Enzymol 274:189–197
Nelson J, Denisenko O, Bomsztyk K (2009) The fast chromatin immunoprecipitation method. Methods Mol Biol 567:45–57
Thorne AW, Myers FA, Hebbes TR (2004) Native chromatin immunoprecipitation. Methods Mol Biol 287:21–44
Orlando V, Strutt H, Paro R (1997) Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 11:205–214
Kuo MH, Allis CD (1999) In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment. Methods 19:425–433
Solomon MJ, Larsen PL, Varshavsky A (1988) Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 53:937–947
Flanagin S, Nelson JD, Castner DG et al (2008) Microplate-based chromatin immunoprecipitation method, Matrix ChIP: a platform to study signaling of complex genomic events. Nucleic Acids Res 36:e17
Solomon MJ, Varshavsky A (1985) Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures. Proc Natl Acad Sci USA 82: 6470–6474
Le May M, Mach H, Lacroix N et al (2011) Contribution of retinoid X receptor signaling to the specification of skeletal muscle lineage. J Biol Chem 286:26806–26812
Barski A, Cuddapah S, Cui K et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823–837
Huebert DJ, Kamal M, O’Donovan A et al (2006) Genome-wide analysis of histone modifications by ChIP-on-chip. Methods 40:365–369
Higazi A, Abed M, Chen J et al (2011) Promoter context determines the role of proteasome in ligand-dependent occupancy of retinoic acid responsive elements. Epigenetics 6:202–211
Acknowledgments
This work was supported by Natural Sciences and Engineering Research Council and Canadian Institutes of Health Research.
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Le May, M., Li, Q. (2013). Analysis of p300 Occupancy at the Early Stage of Stem Cell Differentiation by Chromatin Immunoprecipitation. In: Bina, M. (eds) Gene Regulation. Methods in Molecular Biology, vol 977. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-284-1_25
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DOI: https://doi.org/10.1007/978-1-62703-284-1_25
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Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-283-4
Online ISBN: 978-1-62703-284-1
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