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KMID : 1132720060040010001
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Genomics & Informatics
2006 Volume.4 No. 1 p.1 ~ p.10
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Cloning of NotI-linked DNA Detected by Restriction Landmark Genomic Scanning of Human Genome
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Kim Jeong-Hwan
Lee Kyung-Tae
Kim Hyung-Chul
Yang Jin-Ok
Hahn Yoon-Soo
Kim Sang-Soo
Kim Seon-Young
Yoo Hyang-Sook
Kim Yong-Sung
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Abstract
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Epigenetic alterations are common features of human solid tumors, though global DNA methylation has been difficult to assess. Restriction Landmark Genomic Scanning (RLGS) is one of technology to examine epigenetic alterations at several thousand NotI sites of promoter regions in tumor genome. To assess sequence information for NotI sequences in RLGS gel, we cloned 1,161 unique NotI-linked clones, compromising about 60% of the spots in the soluble region of RLGS profile, and performed BLAT searches on the UCSC genome server, May 2004 Freeze. 1,023 (88%) unique sequences were matched to the CpG islands of human genome showing a large bias of RLGS toward identifying potential genes or CpG islands. The cloned NotI-loci had a high frequency (71%) of occurrence within CpG islands near the 5’ ends of known genes rather than within CpG islands near the 3’ ends or intragenic regions, making RLGS a potent tool for the identification of gene-associated methylation events. By mixing RLGS gels with all NotI-linked clones, we addressed 151 NotI
sequences onto a standard RLGS gel and compared them with previous reports from several types of tumors. We hope our sequence information will be useful to identify novel epigenetic targets in any types of tumor genome
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KEYWORD
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RLGS, epigenetics, cancer, CpG island
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