Abstract
Here we describe an adapted ChIP-on-chip protocol for the analysis of DNA topoisomerase chromosomal binding in Saccharomyces cerevisiae cells. The ChIP-on-chip technique is based on the immunoprecipitation of crosslinked chromatin (ChIP, chromatin immunoprecipitation), followed by DNA amplification and hybridization to high-density oligonucleotide arrays (Chip). Comparison of the signal intensities of immunoprecipitated and control fractions provides a measurement of the protein–DNA association along entire genomes. ChIP-on-chip analysis of DNA topoisomerase binding to chromosomal DNA opens a window to the understanding of the in vivo contribution of these enzymes to the different DNA transactions taking place concomitantly within the context of the highly organized eukaryotic genome. Chromosomal binding profiles obtained from synchronized cells allow scoring the temporal and spatial restriction of these enzymes at different cell cycle stages. By using this approach, novel aspects of DNA topoisomerase function in chromosome metabolism might be unmasked.
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References
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Acknowledgments
Work in M.F. lab is supported by grants from the Associazione Italiana per la Ricerca sul Cancro, Association for International Cancer Research, and, partially, from European Union, Telethon-Italy, and the Italian Ministry of Education. K.S. is supported by a grant of the Genome Network Project and Grant-in-Aid for Scientific Research (S) from the MEXT. Y.K. is supported by Global COE program from MEXT. We thank all the members of our laboratories for helpful discussions and criticisms.
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© 2009 Humana Press, a part of Springer Science+Business Media, LLC
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Bermejo, R., Katou, YM., Shirahige, K., Foiani, M. (2009). ChIP-on-Chip Analysis of DNA Topoisomerases. In: Clarke, D. (eds) DNA Topoisomerases. Methods in Molecular Biology™, vol 582. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-340-4_9
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DOI: https://doi.org/10.1007/978-1-60761-340-4_9
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Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-60761-339-8
Online ISBN: 978-1-60761-340-4
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