Protocol

Epigenetics Protocols

Volume 791 of the series Methods in Molecular Biology pp 101-112

Date:

Restriction Landmark Genome Scanning

  • Hisato OkuizumiAffiliated withGenetic Resources Center, National Institute of Agrobiological Sciences (NIAS) Email author 
  • , Tomoko TakamiyaAffiliated withSchool of Pharmacy, Nihon University
  • , Yasushi OkazakiAffiliated withResearch Center for Genomic Medicine, Saitama Medical University
  • , Yoshihide HayashizakiAffiliated withOmics Science Center, Riken

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Abstract

Restriction landmark genome scanning (RLGS) method is a high-resolution two-dimensional electrophoresis system for analyses of the whole genome DNA which is including methylation status. It has been used for cloning genes of model animals and human genomes, detection of imprinted genes, and genome-wide methylation research in cancer. The conventional RLGS detected both polymorphism and methylated NotI sites between samples. Here, we have developed improved RLGS method with isoschizomer restriction enzymes such as MspI and HpaII to specifically detect methylated sites, using differential sensitivity of the restriction enzymes to methylated sequences. Recently, by using the genome database information, the RLGS spot sites were efficiently identified by this improved method. Then, genome methylation sites of Arabidopsis were mapped, and a unique inheritance was detected in methylated gene in rice. Now, epigenetic research becomes easy with the improved RLGS and it also can be applied for animal genome. Therefore, RLGS method is useful to explore for novel epigenetic phenomenon.

Key words

Restriction landmark genome scanning First dimensional electrophoresis Second ­dimensional electrophoresis Isoschizomer Genome methylation in silico RLGS