Abstract
The method described here is based on a technique developed to analyze the chromatin structure of the SV40 origin of replication, and also alterations in nucleosomal structures in the hsp70 promoter of Drosophila after heat shock (1,2). It relies on the ability of formaldehyde to crosslink proteins and nucleic acids in living cells, from which chromatin can be isolated and protein-DNA interactions probed by immunoprecipitation using specific antibodies.
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References
Solomon, M. J. and Varshavsky, A. (1985) Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures. Proc. Natl. Acad. Sci. USA 82, 6470–6474.
Solomon, M. J., Larsen, P. L., and 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.
McGhee, J. D. and von Hippel, P. H. (1975) Formaldehyde as a probe of DNA structure. I. Reaction with exocyclic amino groups of DNA bases. Biochemistry 14, 1281–1296.
McGhee, J. D. and von Hippel, P. H. (1975) Formaldehyde as a probe of DNA structure. II. Reaction with endocyclic imino groups of DNA bases. Biochemistry 14, 1297–1303.
Orlando, V. and Paro, R. (1993) Mapping Polycomb-repressed domains in the bithorax complex using in vivo formaldehyde crosslinked chromatin. Cell 75, 1187–1198.
Zhao, K., Hart, C. M., and Laemmli, U. K. (1995) Visualisation of chromosomal domains with boundary element-associated factor BEAF-32. Cell 81, 879–889.
Orlando, V., Strutt, H., and Paro, R. (1997) Analysis of chromatin structure by in vivo formaldehyde crosslinking. Methods: A Companion to Methods Enzymol. 11, 205–214.
Strutt, H. L., Cavalli, G., and Paro, R. (1997) Co-localisation of Polycomb protein and GAGA factor on regulatory elements responsible for the maintenance of homeotic gene expression. EMBO J. 16, 3621–3632.
Lüdecke, H.-J., Senger, G., Claussen, U., and Horsthemke, B. (1989) Cloning defined regions of the human genome by microdissection of banded chromosomes and enzymatic amplification. Nature 338, 348–350.
Harlow, E. and Lane, D. (1988) Antibodies: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
Church, G. M. and Gilbert, W. (1984) Genomic sequencing. Proc. Natl. Acad. Sci. USA 81, 1991–1995.
Strutt, H. (1997) In vivo mapping of Polycomb and trithorax group proteins in chromatin of Drosophila melanogaster. PhD thesis, The Open University, UK.
Martin, C. H., Mayeda, C. A., Davis, C. A., Ericsson, C. L., Knafels, J. D., Mathog, D. R., Celniker, S. E., Lewis, E. B., and Palazzolo, M. J. (1995) Complete sequence of the bithorax complex of Drosophila. Proc. Natl. Acad. Sci. USA 92, 8398–8402.
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© 1999 Humana Press Inc.
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Strutt, H., Paro, R. (1999). Mapping DNA Target Sites of Chromatin Proteins In Vivo by Formaldehyde Crosslinking. In: Becker, P.B. (eds) Chromatin Protocols. Methods in Molecular Biology™, vol 119. Humana Press. https://doi.org/10.1385/1-59259-681-9:455
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DOI: https://doi.org/10.1385/1-59259-681-9:455
Publisher Name: Humana Press
Print ISBN: 978-0-89603-665-9
Online ISBN: 978-1-59259-681-2
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