Abstract
Hypomethylation of repetitive DNA elements is a common epigenetics event in cancer. Although it is believed that this hypomethylation impacts chromosomal and transcriptional stability of the genome, the extent of repetitive sequences contribution to the development and progression of human cancers remains to be clarified. Repetitive sequences have largely been ignored by genome-wide studies, and thus little is known about the DNA methylation profiles of different repetitive DNA elements types. As a step toward investigating epigenetic landscape of repetitive DNA, we have developed a repeat-specific DNA microarray called RepArray. The RepArray comprises 236 prototypic oligonucleotides that span the main repetitive elements families found in the human genome. Combined to a methylated DNA immunoprecipitation (MeDIP) approach, RepArray allows depicting simultaneously the global trends that affect multiple repeat classes through the analysis of a restricted number of targets. Here, we present the MeDIP-on-RepArray protocol as it was established in our laboratory to delineate DNA methylation changes after chemical or genetic disruption of DNA methyltransferase activity in cells. It might serve as a workflow guideline for screening DNA methylation changes on repetitive elements during development and aging, among tissues and in various types of stress or pathological situations.
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Acknowledgments
We are grateful to Dr N. Vassetzky, Dr G. Fourel, Pr. P. Barbry, Dr. J. Puechberty, Dr G. Roizes, Pr. C. Vourc’h, Dr F. Devaux, and Pr C. Gautier for their contribution in developing the oligoarray RepArray and the computational tools. This work was supported by European Union 6th framework program grant RISCRAD; ARECA and EpiPro framework programs from Canceropole Lyon Auvergne Rhône Alpes and the Association pour la Recherche sur le Cancer and the Ligue Nationale contre le Cancer (“Equipe Labellisée”).
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Gilson, E., Horard, B. (2012). Comprehensive DNA Methylation Profiling of Human Repetitive DNA Elements Using an MeDIP-on-RepArray Assay. In: Bigot, Y. (eds) Mobile Genetic Elements. Methods in Molecular Biology, vol 859. Humana Press. https://doi.org/10.1007/978-1-61779-603-6_16
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DOI: https://doi.org/10.1007/978-1-61779-603-6_16
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