tailieunhanh - Báo cáo khoa học: Epigenetics: application of virtual image restriction landmark genomic scanning (Vi-RLGS)

Restriction landmark genomic scanning (RLGS) is a powerful method for the systematic detection of genetic mutations in DNA length and epigenetic alteration due to DNA methylation. However, the identification of poly-morphic spots is difficult because the resulting RLGS spots contain very little target DNA and many non-labeled DNA fragments. | ễFEBS Journal MINIREVIEW Epigenetics application of virtual image restriction landmark genomic scanning Vi-RLGS Kuniaki Koike1 Tomoki Matsuyama2 and Toshikazu Ebisuzaki1 1 ComputationalAstrophysics Laboratory Discovery Research Institute RIKEN Saitama Japan 2 Plant Breeding and CellEngineering Research Unit Discovery Research Institute RIKEN Saitama Japan Keywords Arabidopsis DNA methylation DNA polymorphism electrophoresis epigenetics in silico mutant 5mC N6-methyladenine Vi-RLGS Correspondence T. Ebisuzaki ComputationalAstrophysics Laboratory Discovery Research Institute RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan Fax 81 48 467 4078 Tel 81 48 467 9414 E-mail ebisu@ Restriction landmark genomic scanning RLGS is a powerful method for the systematic detection of genetic mutations in DNA length and epigenetic alteration due to DNA methylation. However the identification of polymorphic spots is difficult because the resulting RLGS spots contain very little target DNA and many non-labeled DNA fragments. To overcome this we developed a virtual image restriction landmark genomic scanning Vi-RLGS system to compare actual RLGS patterns with computer-simulated RLGS patterns virtual RLGS patterns . Here we demonstrate in detail the contents of the simulation program rlgssim based on the linear relationship between the reciprocal of mobility plotted against DNA fragment length and Vi-RLGS profiling of Arabidopsis thaliana. Received 30 November 2007 revised 28 January 2008 accepted 1 February 2008 doi Restriction landmark genomic scanning RLGS uses restriction enzyme sites as landmarks 1 2 and is used in the detection of DNA polymorphisms caused by genetic mutations and hyper- or hypomethylation changes in cancer cells 3-6 imprinted genes 7 8 and linkage maps 9 10 . This method is an especially powerful tool in DNA methylation studies using methylation-sensitive restriction enzymes as it allows genome-wide scanning to detect .