Abstract
Methylated DNA immunoprecipitation (MeDIP) is an immunocapturing approach for unbiased enrichment of DNA that is methylated on cytosines. The principle is that genomic DNA is randomly sheared by sonication and immunoprecipitated with an antibody that specifically recognizes 5-methylcytidine (5mC), which can be combined with PCR or high-throughput analysis (microarrays, deep sequencing). The MeDIP technique has been originally used to generate DNA methylation profiles on a genome scale in mammals and plants. Here we provide an optimized version of the MeDIP protocol suitable for low amounts of DNA, which can be used to study DNA methylation in cellular populations available in small quantities.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Meissner A (2010) Epigenetic modifications in pluripotent and differentiated cells. Nat Biotechnol 28:1079–1088
Laird PW (2010) Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 11:191–203
Lister R, Pelizzola M, Dowen RH et al (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315–322
Weber M, Davies JJ, Wittig D et al (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37:853–862
Down TA, Rakyan VK, Turner DJ et al (2008) A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 26:779–785
Pelizzola M, Koga Y, Urban AE et al (2008) MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. Genome Res 18:1652–1659
Chavez L, Jozefczuk J, Grimm C et al (2010) Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Res 20:1441–1450
Mohn F, Weber M, Schubeler D et al (2009) Methylated DNA immunoprecipitation (MeDIP). Methods Mol Biol 507:55–64
Borgel J, Guibert S, Li Y et al (2010) Targets and dynamics of promoter DNA methylation during early mouse development. Nat Genet 42:1093–1100
Jia J, Pekowska A, Jaeger S et al (2010) Assessing the efficiency and significance of methylated DNA immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA. BMC Res Notes 3:240
Li N, Ye M, Li Y et al (2010) Whole genome DNA methylation analysis based on high throughput sequencing technology. Methods 52:203–212
Harris RA, Wang T, Coarfa C et al (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 28:1097–1105
Acknowledgments
This work was supported by the CEFIC Long Research Initiative (LRI-EMSG49-CNRS-08).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Borgel, J., Guibert, S., Weber, M. (2012). Methylated DNA Immunoprecipitation (MeDIP) from Low Amounts of Cells. In: Engel, N. (eds) Genomic Imprinting. Methods in Molecular Biology, vol 925. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-011-3_9
Download citation
DOI: https://doi.org/10.1007/978-1-62703-011-3_9
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-010-6
Online ISBN: 978-1-62703-011-3
eBook Packages: Springer Protocols