International Mammalian Genome Society

17th International Mouse Genome Conference

9-12 November 2003, Braunschweig, Germany


POSTER 140 - COMPUTATIONAL SOFTWARE FOR RESTRICTION LANDMARK GENOMIC SCANNING (RLGS) AND THE APPLICATION FOR MOUSE GENOME-WIDE METHYLATION SCREENING

Kimura MT
Roswell Park Cancer Institute

Co-Authors: 1) Song F, 1) Okada H, 2) Matsuyama T, 1) Held W A, 1) Nagase H
Institutions: 1) Roswell Park Cancer Institute, 2) RIKEN (The Institute of Physical and Chemical Research)

DNA cytosine 5' methylation relates to various biological phenotypes such as regulation of gene transcription, genomic imprinting, DNA replication timing, and chromatin structure in mammalian cells. To identify DNA methylation changes that cause biological phenomena such as carcinogenesis, we have analysed mouse genome-wide methylation patterns by methylation sensitive Restriction Landmark Genomic Scanning (MS-RLGS). RLGS is a method for the two-dimensional display of 1,500-2,000 end-labelled DNA restriction fragments at one try. Genome-wide DNA methylation status can be analysed by RLGS with methylation-sensitive restriction enzymes. However, there are some difficulties to analyse 1,500-2,000 RLGS spots.

To facilitate RLGS data analysis, we have developed computational software, Virtual image RLGS (Vi-RLGS). Vi-RLGS analyses the total genome sequence information, and indicates consequent RLGS spot patterns digested by restriction enzymes and DNA sequence information of each spots. We have confirmed that most of Vi-RLGS spots corresponded to real RLGS spots by PCR and sequencing experiments. Thus, Vi-RLGS is practicable for identification of DNA sequences of RLGS spots.

Our mission is to complete the DNA methylation map in mouse and to reveal DNA methylation changes that relate to carcinogenesis. We have analysed methylation status of brain, lung, liver, kidney, muscle, liver, skin, and testis tissues in several laboratory mouse strains. These results have revealed genomic sites which are differentially methylated among tissues and strains. Furthermore, we have found multiple aberrant RLGS spots observed in mouse liver cancer. Results from these studies will be presented.


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