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CpG Islands pp 157-174 | Cite as

Genome-Wide Profiling of DNA Methyltransferases in Mammalian Cells

  • Massimiliano Manzo
  • Christina Ambrosi
  • Tuncay Baubec
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1766)

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.

Key words

ChIP-seq Immunoprecipitation In vivo biotinylation Next-generation sequencing DNA methyltransferases CpG islands 

Notes

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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Massimiliano Manzo
    • 1
    • 2
  • Christina Ambrosi
    • 1
    • 2
  • Tuncay Baubec
    • 1
  1. 1.Department of Molecular Mechanisms of DiseaseUniversity of ZurichZurichSwitzerland
  2. 2.Molecular Life Science PhD Program of the Life Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland

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