Cloning of Notl-linked DNA detected by restriction landmark genomic scanning of human genome

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Title
Cloning of Notl-linked DNA detected by restriction landmark genomic scanning of human genome
Author(s)
Jeong Hwan Kim; Kyung-Tae Lee; Hyung-Chul Kim; Jin Ok Yang; Y Hahn; S Kim; Seon-Young Kim; Hyang Sook Yoo; Yong Sung Kim
Bibliographic Citation
Genomics & Informatics, vol. 4, no. 1, pp. 1-10
Publication Year
2006
Abstract
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.
Keyword
RLGSepigeneticscancerCpG island
ISSN
I000-0158
Publisher
Korea Soc-Assoc-Inst
Type
Article
Appears in Collections:
Aging Convergence Research Center > 1. Journal Articles
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