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Nucleic Acids Research, 2003, Vol. 31, No. 15 4490-4496
© 2003 Oxford University Press

Global methylation screening in the Arabidopsis thaliana and Mus musculus genome: applications of virtual image restriction landmark genomic scanning (Vi-RLGS)

Tomoki Matsuyama1, Makoto T. Kimura4, Kuniaki Koike2, Tomoko Abe1, Takeshi Nakano1, Tadao Asami1, Toshikazu Ebisuzaki2, William A. Held5, Shigeo Yoshida1,3 and Hiroki Nagase*,4

1 Plant Functions Laboratory, 2 Computational Science Division and 3 Plant Science Center, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-0198, Japan and 4 Cancer Genetics and 5 Molecular Cellular Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA

*To whom correspondence should be addressed. Tel: +1 716 845 1546; Fax: +1 716 845 1698; Email: hiroki.nagase{at}roswellpark.org
Correspondence may also be addressed to Shigeo Yoshida. Tel: +81 48 462 4674; Fax: +81 48 467 9524; Email: yshigeo{at}postman.riken.go.jp

Understanding the role of ‘epigenetic’ changes such as DNA methylation and chromatin remodeling has now become critical in understanding many biological processes. In order to delineate the global methylation pattern in a given genomic DNA, computer software has been developed to create a virtual image of restriction landmark genomic scanning (Vi-RLGS). When using a methylation- sensitive enzyme such as NotI as the restriction landmark, the comparison between real and in silico RLGS profiles of the genome provides a methylation map of genomic NotI sites. A methylation map of the Arabidopsis genome was created that could be confirmed by a methylation-sensitive PCR assay. The method has also been applied to the mouse genome. Although a complete methylation map has not been completed, a region of methylation difference between two tissues has been tested and confirmed by bisulfite sequencing. Vi-RLGS in conjunction with real RLGS will make it possible to develop a more complete map of genomic sites that are methylated or demethylated as a consequence of normal or abnormal development.


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