Optimized design and data analysis of tag-based cytosine methylation assays

Masako Suzuki, Qiang Jing, Daniel Lia, Marién Pascual, Andrew McLellan, John M. Greally

Research output: Contribution to journalArticle

65 Scopus citations

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.

Original languageEnglish (US)
Article numberr36
JournalGenome biology
Volume11
Issue number4
DOIs
StatePublished - Apr 1 2010

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ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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