Mobile Genetic Elements

Volume 859 of the series Methods in Molecular Biology pp 267-291


Comprehensive DNA Methylation Profiling of Human Repetitive DNA Elements Using an MeDIP-on-RepArray Assay

  • Eric GilsonAffiliated withLaboratory of Biology and Pathology of Genomes, CNRS UMR 6267, Institut National de la Santé et de la Recherche Médicale U998, University of Nice Sophia-AntipolisDepartment of Medical Genetics, Centre Hospitalier Universitaire of Nice
  • , Béatrice HorardAffiliated withCentre de Génétique et de Physiologie Moléculaire et Cellulaire-UMR CNRS 5534, Université LYON 1 Email author 

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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.

Key words

DNA methylation 5-Methylcytosine (5mC) antibody DNA repetitive sequences DNA repeats Transposable elements DNA satellite Oligonucleotide microarray MeDIP-on-chip Epigenetics