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.
Publication types
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Evaluation Study
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Research Support, N.I.H., Extramural
MeSH terms
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Base Sequence
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Cells, Cultured
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Cytosine / chemistry
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Cytosine / metabolism*
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DNA Methylation
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DNA-Cytosine Methylases / chemistry
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DNA-Cytosine Methylases / metabolism
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Genome, Human
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Humans
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Polymorphism, Genetic
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Sequence Analysis, DNA*
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Site-Specific DNA-Methyltransferase (Adenine-Specific) / chemistry
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Site-Specific DNA-Methyltransferase (Adenine-Specific) / metabolism
Substances
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Cytosine
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DNA modification methylase EcoP15I
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DNA modification methylase HpaII
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DNA-Cytosine Methylases
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Site-Specific DNA-Methyltransferase (Adenine-Specific)