Abstract
Chromatin immunoprecipitation (ChIP) has been developed for studying protein–DNA interactions and has been extensively used for mapping the localization of posttranslationally modified histones, histone variants, transcription factors, or chromatin modifying enzymes at a given locus or on a genome-wide scale. ChIP methods have been modified and improved over the years to fit a variety of different cell types and tissues. Here, we present a detailed protocol for hippocampal ChIP, of both minced tissue and enzyme-separated hippocampal cells. This protocol enables to study chromatin–protein interactions in a specified population of hippocampal cells, allowing to study chromatin regulation in the central nervous system in a variety of conditions and disorders. Our assay has been developed for histone modifications but is suited for any chromatin binding protein for which specific ChIP-grade antibodies are available.
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
Similar content being viewed by others
References
Huang, L. T., Holmes, G. L., Lai, M. C., Hung, P. L., Wang, C. L., Wang, T. J., Yang, C. H., Liou, C. W., and Yang, S. N. (2002) Maternal deprivation stress exacerbates cognitive deficits in immature rats with recurrent seizures. Epilepsia 43 1141–1148.
Crosio, C., Heitz, E., Allis, C. D., Borrelli, E., and Sassone-Corsi, P. (2003) Chromatin remodeling and neuronal response: multiple signaling pathways induce specific histone H3 modifications and early gene expression in hippocampal neurons. J Cell Sci 116 4905–4914.
Guan, Z., Giustetto, M., Lomvardas, S., Kim, J. H., Miniaci, M. C., Schwartz, J. H., Thanos, D., and Kandel, E. R. (2002) Integration of long-term-memory-related synaptic plasticity involves bidirectional regulation of gene expression and chromatin structure. Cell 111 483–493.
Dedon, P. C., Soults, J. A., Allis, C. D., and Gorovsky, M. A. (1991) A simplified formaldehyde fixation and immunoprecipitation technique for studying protein-DNA interactions. Anal Biochem 197 83–90.
Oneill, L. P., and Turner, B. M. (1996) Immunoprecipitation of chromatin. Methods Enzymol 274, 189–197.
Kuo, M. H., and Allis, C. D. (1999) In vivo cross-linking and immunoprecipitation for studying dynamic protein: DNA associations in chromatin environment. Methods 19 425–433.
Jenuwein, T., and Allis, C. D. (2001) Translating the histone code. Science 293 1074–1080.
Nelson, J. D., Denisenko, O., and Bomsztyk, K. (2006) Protocol for the fast chromatin immunoprecipitation (ChIP) method. Nat Protoc 1 179–185.
Attema, J. L., Papathanasiou, P., Forsberg, E. C., Xu, J., Smale, S. T., and Weissman, I. L. (2007) Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis. Proc Natl Acad Sci USA. 104 12371–12376.
Collas, P., and Dahl, J. A. (2008) Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation. Frontiers in Bioscience 13 929–943.
Dahl, J. A., and Collas, P. (2008) mu ChIP - a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies. Nucleic Acids Res 36 e15.
Dahl, J. A., and Collas, P. (2007) A quick and quantitative chromatin immunoprecipitation assay for small cell samples. Front Biosci. 12 4925–4931.
Barski, A., and Zhao, K. (2009) Genomic Location Analysis by ChIP-Seq. J Cell Biochem 107 11–18.
Thorne, A. W., Myers, F. A., and Hebbes, T. R. (2004) Native chromatin immunoprecipitation. Methods Mol Biol 287 21–44.
Kaech, S., and Banker, G. (2006) Culturing hippocampal neurons. Nat Protoc 1 2406–2415.
Acknowledgments
EM is a Joseph H. and Belle R. Braun Senior Lecturer in Life Sciences and is supported by the Israel Science Foundation (ISF 215/07 and 943/09), the Israel Ministry of Health (6007), the European Union (IRG-206872) and the National Institute for Psychobiology in Israel. TT is supported by the CDA of the International Human Frontier Science Program Organization. BSS is a Safra fellow.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Sailaja, B.S., Takizawa, T., Meshorer, E. (2012). Chromatin Immunoprecipitation in Mouse Hippocampal Cells and Tissues. In: Vancura, A. (eds) Transcriptional Regulation. Methods in Molecular Biology, vol 809. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-376-9_24
Download citation
DOI: https://doi.org/10.1007/978-1-61779-376-9_24
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-61779-375-2
Online ISBN: 978-1-61779-376-9
eBook Packages: Springer Protocols