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

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

doi:10.1186/gb-2010-11-4-r36

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 journal › Article › peer-review

74 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 language	English
Article number	r36
Journal	Genome Biology
Volume	11
Issue number	4
DOIs	https://doi.org/10.1186/gb-2010-11-4-r36
State	Published - 1 Apr 2010
Externally published	Yes

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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.",

author = "Masako Suzuki and Qiang Jing and Daniel Lia and Mari{\'e}n Pascual and Andrew McLellan and Greally, {John M.}",

note = "Funding Information: This work is supported by a grant from the National Institute of Health (NIH, R01 HG004401) to JMG. The authors thank Shahina Maqbool PhD, Raul Olea and Gael Westby of the Einstein Epigenomics Shared Facility for their contributions, Drs Eric Bouhassira and Emmanuel Olivier (Einstein) for the WA01/H1 human ES cell line, and Einstein's Center for Epigenomics.",

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AU - Suzuki, Masako

AU - Jing, Qiang

AU - Lia, Daniel

AU - Pascual, Marién

AU - McLellan, Andrew

AU - Greally, John M.

N1 - Funding Information: This work is supported by a grant from the National Institute of Health (NIH, R01 HG004401) to JMG. The authors thank Shahina Maqbool PhD, Raul Olea and Gael Westby of the Einstein Epigenomics Shared Facility for their contributions, Drs Eric Bouhassira and Emmanuel Olivier (Einstein) for the WA01/H1 human ES cell line, and Einstein's Center for Epigenomics.

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N2 - 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.

AB - 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.

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

Abstract

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