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Whole Genome Methylation Scanning Based on phi29 Polymerase Amplification

R. Brooks1, R. J. Rose1, M. B. Sheahan1, and S. Kurdyukov1,2*

1Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, 2308, Australia; fax: +61-2-4921-5472; E-mail: sergey.kurdyukov@sydney.edu.au; robert.brooks@uon.edu.au; ray.rose@newcastle.edu.au; michael.sheahan@newcastle.edu.au

2Present address: Kolling Institute of Medical Research, Kolling Building, Royal North Shore Hospital, St. Leonards, New South Wales, 2065, Australia

* To whom correspondence should be addressed.

Received November 29, 2010; Revision received February 2, 2011
Identifying differences in DNA methylation is critical to understanding how epigenetics influences gene expression during processes such as development. Here, we propose a method that employs a single, methylation-sensitive restriction endonuclease of choice, to produce discrete pools of methylated and unmethylated DNA from the same sample. A pool of restriction fragments representing unmethylated regions of the genome is first obtained by digestion with a methylation-sensitive endonuclease. The restriction-digested DNA is then concatamerized in the presence of stuffer-adaptor DNA, which prevents interference from originally unmethylated DNA by blocking the ends of the restriction fragments. The concatamerized DNA is amplified by phi29 polymerase to remove methylation marks, and again digested with the same endonuclease to produce a pool of DNA fragments representing methylated portions of the genome. The two pools of DNA fragments thus obtained can be analyzed by end-sequencing or hybridization to a genomic array. In this report we detail a proof of concept experiment that demonstrates the feasibility of our method.
KEY WORDS: whole genome methylation, phi29 polymerase, whole genome amplification, next-generation sequencing

DOI: 10.1134/S0006297911090021