Abstract
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is currently the method of choice to determine binding sites of chromatin-associated factors in a genome-wide manner. Here, we describe a method to investigate the binding preferences of mammalian DNA methyltransferases (DNMT) based on ChIP-seq using biotin-tagging. Stringent ChIP of DNMT proteins based on the strong interaction between biotin and avidin circumvents limitations arising from low antibody specificity and ensures reproducible enrichment. DNMT-bound DNA fragments are ligated to sequencing adaptors, amplified and sequenced on a high-throughput sequencing instrument. Bioinformatic analysis gives valuable information about the binding preferences of DNMTs genome-wide and around promoter regions. This method is unconventional due to the use of genetically engineered cells; however, it allows specific and reliable determination of DNMT binding.
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Acknowledgments
We thank Isabel Schwarz and Joël Wirz for carefully reading the manuscript prior to submission. Research in the Baubeclab is supported by an SNSF Professorship (SNF157488) and Systems-X.ch Special Opportunities Grant (2015_322) to T.B., and by the University of Zurich.
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Manzo, M., Ambrosi, C., Baubec, T. (2018). Genome-Wide Profiling of DNA Methyltransferases in Mammalian Cells. In: Vavouri, T., Peinado, M. (eds) CpG Islands. Methods in Molecular Biology, vol 1766. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7768-0_9
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DOI: https://doi.org/10.1007/978-1-4939-7768-0_9
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