title: Optimized design and data analysis of tag-based cytosine methylation assays.
abstract: Using the type III restriction-modification enzyme EcoP15I, we isolated sequences flanking sites digested by the methylation-sensitive HpaII enzyme or its methylation-insensitive MspI isoschizomer for massively parallel sequencing. A novel data transformation allows us to normalise HpaII by MspI counts, resulting in more accurate quantification of methylation at >1.8 million loci in the human genome. This HELP-tagging assay is not sensitive to sequence polymorphism or base composition and allows exploration of both CG-rich and depleted genomic contexts.
authors.affiliation: Department of Genetics (Computational Genetics), Center for Epigenomics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA.
authors.forename: Masako
authors.initials: M
authors.lastname: Suzuki
authors.forename: Qiang
authors.initials: Q
authors.lastname: Jing
authors.forename: Daniel
authors.initials: D
authors.lastname: Lia
authors.forename: Marién
authors.initials: M
authors.lastname: Pascual
authors.forename: Andrew
authors.initials: A
authors.lastname: McLellan
authors.forename: John M
authors.initials: JM
authors.lastname: Greally
mesh_terms: D001483:Base Sequence; D002478:Cells, Cultured; D003596:Cytosine / Q000737:chemistry / Q000378:metabolism*; D019175:DNA Methylation; D015257:DNA-Cytosine Methylases / Q000737:chemistry / Q000378:metabolism; D015894:Genome, Human; D006801:Humans; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000737:chemistry / Q000378:metabolism
chemical_list: D003596:Cytosine; C089712:DNA modification methylase EcoP15I; C029641:DNA modification methylase HpaII; D015257:DNA-Cytosine Methylases; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific)