title: AutoMeDIP-seq: a high-throughput, whole genome, DNA methylation assay.
abstract: DNA methylation is an epigenetic mark linking DNA sequence and transcription regulation, and therefore plays an important role in phenotypic plasticity. The ideal whole genome methylation (methylome) assay should be accurate, affordable, high-throughput and agnostic with respect to genomic features. To this end, the methylated DNA immunoprecipitation (MeDIP) assay provides a good balance of these criteria. In this Methods paper, we present AutoMeDIP-seq, a technique that combines an automated MeDIP protocol with library preparation steps for subsequent second-generation sequencing. We assessed recovery of DNA sequences covering a range of CpG densities using in vitro methylated λ-DNA fragments (and their unmethylated counterparts) spiked-in against a background of human genomic DNA. We show that AutoMeDIP is more reliable than manual protocols, shows a linear recovery profile of fragments related to CpG density (R(2)=0.86), and that it is highly specific (>99%). AutoMeDIP-seq offers a competitive approach to high-throughput methylome analysis of medium to large cohorts.
authors.affiliation: UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London WC1E 6BT, UK. l.butcher@ucl.ac.uk
authors.forename: Lee M
authors.initials: LM
authors.lastname: Butcher
authors.forename: Stephan
authors.initials: S
authors.lastname: Beck
mesh_terms: D000906:Antibodies / Q000276:immunology; D004247:DNA / Q000737:chemistry / Q000276:immunology / Q000378:metabolism; D019175:DNA Methylation; D015894:Genome, Human / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods*; D011786:Quality Control; D015203:Reproducibility of Results
chemical_list: D000906:Antibodies; D004247:DNA
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