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Genome-Wide Analysis of Methylation in Bovine Clones by Methylated DNA Immunoprecipitation (MeDIP)

Part of the Methods in Molecular Biology book series (MIMB,volume 1222)

Abstract

Methylated DNA immunoprecipitation (MeDIP), when coupled to high-throughput sequencing or microarray hybridization, allows for the identification of methylated loci at a genome-wide scale. Genomic regions affected by incomplete reprogramming after nuclear transfer can potentially be delineated by comparing the MeDIP profiles of bovine clones and non-clones. This chapter presents a MeDIP protocol largely inspired from Mohn and colleagues (Mohn et al., Methods Mol Biol 507:55–64, 2009), with PCR primers specific for cattle, and when possible, overviews of experimental designs adapted to the comparison between clones and non-clones.

Key words

  • Cattle
  • Clones
  • Nuclear transfer
  • DNA methylation
  • MeDIP
  • Microarray
  • Epigenomics
  • CpG
  • Genome-wide analysis

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Acknowledgements

This work has been funded by INRA (PHASE ACI 2010) and by grant ANR-09-GENM-012-01 (French National Research Agency/APIS-GENE).

The author would like to thank Sean Kennedy and the MetaQuant platform (MICALIS, INRA, Jouy-en-Josas, France) for their help with DNA sonication; Sandrine Balzergue and the transcriptomic platform (URGV, INRA, Evry, France) for their help with microarray hybridizations; Luc Jouneau (VIM/BDR, INRA, Jouy-en-Josas, France) for statistical analysis and Hélène Jammes and all team members (BDR, INRA, Jouy-en-Josas, France) for everyday support and helpful discussions.

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Correspondence to Hélène Kiefer .

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Kiefer, H. (2015). Genome-Wide Analysis of Methylation in Bovine Clones by Methylated DNA Immunoprecipitation (MeDIP). In: Beaujean, N., Jammes, H., Jouneau, A. (eds) Nuclear Reprogramming. Methods in Molecular Biology, vol 1222. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1594-1_20

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  • DOI: https://doi.org/10.1007/978-1-4939-1594-1_20

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  • Publisher Name: Humana Press, New York, NY

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