title: Comprehensive DNA methylation profiling of human repetitive DNA elements using an MeDIP-on-RepArray assay.
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.
authors.affiliation: Laboratory of Biology and Pathology of Genomes, CNRS UMR 6267, Institut National de la Santé et de la Recherche Médicale U998, University of Nice Sophia-Antipolis, Nice, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Gilson
authors.forename: Béatrice
authors.initials: B
authors.lastname: Horard
mesh_terms: D004247:DNA / Q000302:isolation & purification; D053837:DNA Cleavage; D019175:DNA Methylation; D004251:DNA Transposable Elements / Q000235:genetics*; D005456:Fluorescent Dyes / Q000737:chemistry; D015894:Genome, Human; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D013010:Sonication; D013194:Staining and Labeling / Q000379:methods
chemical_list: D004251:DNA Transposable Elements; D005456:Fluorescent Dyes; D004247:DNA