International Mammalian Genome Society

The 16th International Mouse Genome Conference (2002)


POSTER 22 - GENOME-WIDE METHYLATION SCREENING IN MOUSE GENOME: AN APPLICATION TO MOUSE LIVER CANCER

M T K Kimura
Roswell Park Cancer Institute

2) Matuyama T, 1) Held WA, 2) Yoshida S, 1) Nagase H
1) Roswell Park Cancer Institute, 2) RIKEN

Epigenetic DNA modification such as DNA methylation within CpG islands relates to various biological phenotypes such as transcriptional regulation, DNA replication timing, chromatin condensation, and genomic imprinting. However, the genome-wide methylation pattern has not been examined efficiently. Restriction Landmark Genomic Scanning (RLGS) is a method for the two-dimensional display of end labeled DNA restriction fragments. RLGS, with methylation sensitive restriction enzymes such as NotI, BssHII, and XmaIII, reveals random screenings of DNA methylation, which covers around 1% of the genome in a RLGS gel. It is, however, difficult to identify sequences from aberrant methylated RLGS spots. To facilitate systematic analysis of RLGS data, we have developed a computational tool, Virtual RLGS (Vi-RLGS), which is based on mouse genomic DNA sequence information from sequence databases. Vi-RLGS software predicts RLGS two-dimensional electrophoretogram patterns and the DNA sequences of the RLGS signal spots. We have examined the sequences of real RLGS signal spots and have confirmed those spots containing the sequences predicted by the Vi-RLGS software. So far, we have found uncharacterized DNA methylations: CpG islands on chromosome 3 and 17 were hypermethylated in mouse liver tumors. The further examination on these alternations and utilization of Vi-RLGS will be discussed.


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