Global methylation screening in the Arabidopsis thaliana and Mus musculus genome: applications of virtual image restriction landmark genomic scanning (Vi-RLGS).
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.
Matsuyama
Tomoki
T
Plant Functions Laboratory, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-0198, Japan.
Kimura
Makoto T
MT
Koike
Kuniaki
K
Abe
Tomoko
T
Nakano
Takeshi
T
Asami
Tadao
T
Ebisuzaki
Toshikazu
T
Held
William A
WA
Yoshida
Shigeo
S
Nagase
Hiroki
H
D000818:Animals; D017360:Arabidopsis / Q000235:genetics*; D019175:DNA Methylation; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism; D016678:Genome; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D051379:Mice / Q000235:genetics*; D008810:Mice, Inbred C57BL; D009928:Organ Specificity; D015183:Restriction Mapping / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D015252:Deoxyribonucleases, Type II Site-Specific; C038565:GCGGCCGC-specific type II deoxyribonucleases