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PMID: 20359321 Published · ppublish English Evaluation Study Journal Article Research Support, N.I.H., Extramural

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

Genome biology ·Vol. 11 ·No. 4 ·2010-00-00 ·Pages R36

Suzuki M, Jing Q, Lia D, Pascual M, McLellan A, Greally JM

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.

MeSH Terms

Base Sequence Cells, Cultured Cytosine/chemistry,metabolism DNA Methylation DNA-Cytosine Methylases/chemistry,metabolism Genome, Human Humans Polymorphism, Genetic Sequence Analysis, DNA Site-Specific DNA-Methyltransferase (Adenine-Specific)/chemistry,metabolism

Chemicals

Cytosine DNA modification methylase EcoP15I DNA modification methylase HpaII DNA-Cytosine Methylases Site-Specific DNA-Methyltransferase (Adenine-Specific)

Authors & Affiliations

6 authors, click to expand affiliations / ORCID

Suzuki Masako

Department of Genetics (Computational Genetics), Center for Epigenomics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA.

Jing Qiang

Lia Daniel

Pascual Marién

McLellan Andrew

Greally John M

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Article Info

Journal

Genome biology

Abbr.

Genome Biol

ISSN

1474-760X

DOI

10.1186/gb-2010-11-4-r36

Published

2010-00-00

Epub

2010-00-01

Pages

R36

Language

English

Region

England

NLM ID

100960660

PMCID

PMC2884539

Subset

Grants

NHGRI NIH HHS · R01 HG004401 · United States

External Links

PubMed source DOI: 10.1186/gb-2010-11-4-r36 PMC Full Text View journal details

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