Genomics & Informatics

Korea Genome Organization (한국유전체학회)
권호 표지

Cloning of Notl-linked DNA Detected by Restriction Landmark Genomic Scanning of Human Genome

  • Kim Jeong-Hwan (Human Genomics Laboratory, Genome Research Center) ;
  • Lee Kyung-Tae (Human Genomics Laboratory, Genome Research Center) ;
  • Kim Hyung-Chul (Human Genomics Laboratory, Genome Research Center) ;
  • Yang Jin-Ok (National Genome Information Center) ;
  • Hahn Yoon-Soo (Human Genomics Laboratory, Genome Research Center) ;
  • Kim Sang-Soo (National Genome Information Center, Department of Bioinformatics, Soongsil University) ;
  • Kim Seon-Young (Human Genomics Laboratory, Genome Research Center) ;
  • Yoo Hyang-Sook (The Center for Functional Analysis of Human Genome, 21 st Century Frontier R&D Program) ;
  • Kim Yong-Sung (Human Genomics Laboratory, Genome Research Center, Department of Functional Genomics, University of Science & Technology, Korea Research Institute of Bioscience and Biotechnology)
  • Published : 2006.03.01
Download PDF
⟨ Previous Next ⟩

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 Notl sites of promoter regions in tumor genome. To assess sequence information for Notl sequences in RLGS gel, we cloned 1,161 unique Notl-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 Notl-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 Notl-linked clones, we addressed 151 Notl 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.

Keywords

References

  1. Baylin, S.B., Herman, J.G., Graff, J.R., Vertino, P.M., and Issa, J.P. (1998). Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv. Cancer Res. 72, 141-196
  2. Brown, R. and Strathdee, G. (2002). Epigenomics and epigenetic therapy of cancer. Trends Mol. Med. 8, S43-S48 https://doi.org/10.1016/S1471-4914(02)02314-6
  3. Costello, J.F., Fruhwald, M.C., Smiraglia, D.J., Rush, L.J., Robertson, G.P., et al. (2000). Aberrant CpG-island methylation has non-random and tumor-type-specific patterns. Nat. Genet. 24, 132-138 https://doi.org/10.1038/72785
  4. Cho, M., Konishi, N., Yamamoto, K., Inui, T., Kitahori, Y., Nakagawa, Y., Uemura, H., Hirao, Y., and Hiasa, Y. (1998). Genomic Aberrations in Renal Cell Carcinomas Detected by Restriction Landmark Genomic Scanning. Eur. J. Cancer. 34, 2112-2118 https://doi.org/10.1016/S0959-8049(98)00261-5
  5. Dai, Z., Lakshmanan, R.R., Zhu, W.G., Smiraglia, D.J., Rush, L.J., Fruhwald, M.C., Brena, R.M., Li, B., Wright, F.A., Ross, P., Otterson, G.A., and Plass, C. (2001). Global Methylation Profiling of Lung Cancer Identifies Novel Methylated Genes. Neoplasia 3, 1-10
  6. Dai, Z., Weichenhan, D., Wu, Y.Z., Hall, J.L., Rush, L.J., Smith, L.T., Raval, A., Yu, L., Kroll, D., Muehlisch, J., Fruhwald, M.C., de Jong, P., Catanese, J., Davuluri, R.V., Smiraglia, D.J., and Plass, C. (2002). An Asci boundary library for the studies of genetic and epigenetic alterations in CpG islands. Genome Res. 12, 1591-1598 https://doi.org/10.1101/gr.197402
  7. Hatada, I., Hayashizaki, Y., Hirotsune, S., Komatsubara, H., and Mukai, T. (1991). A genomic scanning method for higher organisms using restriction sites as landmark. Proc. Natl. Acad. Sci. USA 88, 9523-9527
  8. Hayashizaki, Y., Hirotsune, S., Okazaki, Y., Hatada, I., Shibata, H., Kawai, J., Hirose, K., Watanabe, S., Fushiki, S., and Wada, S. (1993). Restriction landmark genomic scanning method and its various applications. Electrophoresis 14, 251-258 https://doi.org/10.1002/elps.1150140145
  9. Jones, P.A. and Laird, P.W. (1999). Cancer epigenetics comes of age. Nat. Genet. 21, 163-167 https://doi.org/10.1038/5947
  10. Jones, P.A. and Baylin, S.B. (2002). The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 3, 415-428 https://doi.org/10.1038/nrg816
  11. Kim, Y.S., Yoo, H.S., Lee, K.T., Goh, S.H., Jung, J.S., Oh, S.W., Baba, M, Yasuda, T., Matsubara, K. and Nagai, H. (2000). Detection of genetic alternations in the human gastric cancer cell lines by two-dimensional analysis of genomic DNA. Int. J. Oncol. 17,297-308
  12. Kuick, R., Asakawa, J., Neel, J.V., Kodaira, M., Satoh, C., Thoraval, D., Gonzalez, I.L., and Hanash, S.M. (1996). Studies of the inheritance of human ribosomal DNA variants detected in two-dimensional separations of genomic restriction fragments. Genetics 144, 307-116
  13. Laird, P.W. (2003). The power and the promise of DNA methylation markers. Nat. Rev. Cancer 3, 253-266 https://doi.org/10.1038/nrc1045
  14. Miwa, W., Yashima, K., Sekine, T., and Sekiya, T. (1995). Demethylation of a repetitive DNA sequence in human cancers. Electrophoresis 16, 227-232 https://doi.org/10.1002/elps.1150160138
  15. Momparler, R.L., Bouffard, D.Y., Momparler, L.F., Dionne,J., Belanger, K., and Ayoub, J. (1997). Pilot phase I-II study on 5-aza-2'-deoxycytidine (Decitabine) in patients with metastatic lung cancer. Anticancer Drugs 8, 358-368 https://doi.org/10.1097/00001813-199704000-00008
  16. Nagai, H., Ponglikitmongkol, M., Mita, E., Ohmachi, Y., Yoshikawa, H., Saeki, R., Yumoto, Y., Nakanishi, T., and Matsubara, K. (1994). Aberration of genomic DNA in association with human hepatocellular carcinomas detected by 2-dimensional gel analysis. Cancer Res. 54, 1545-1550
  17. Nakamura, M., Konishi, N.,Tsunoda, S., Hiasa,Y., Tsuzuki, T., Takemura,K., Kobitsu, K., and Sakaki,T. (1997).Genomic alterations in humanglioma cell lines detected by restriction landmark genomic scanning. J. Neurooncol. 34, 203-209 https://doi.org/10.1023/A:1005714811327
  18. Ohsumi, T., Okazaki, Y., Hirotsune, S., Shibata, H., Muramatsu, M., Suzuki, H., Taga, C., Watanabe, S., and Hayashizaki, Y. (1995). A spot cloning method for restriction landmark genomic scanning. Electrophoresis 16, 203-209 https://doi.org/10.1002/elps.1150160135
  19. Okazaki, Y., Okuizumi, H., Ohsumi, T., Nomura, O., Takada, S., Kamiya, M., Sasaki, N., Matsuda, Y., Nishimura, M., Tagaya, O., Muramatsu, M., and Hayashizaki, Y. (1996). A genetic linkage map of the Syrian hamster and localization of cardiomyopathy locus on chromosome 9qa2.1-b1 using RLGS spot-mapping. Nat. Genet. 13, 87-90 https://doi.org/10.1038/ng0596-87
  20. Okuizumi, H., Okazaki, Y., Ohsumi, T., Hanami, T., Mizuno, Y., Muramatsu, M., Hayashizaki, Y., Plass, C., and Chapman, V.M. (1995). A single gel analysis of 575 dominant and codominant restriction landmark genomic scanning loci in mice interspecific backcross progeny. Electrophoresis 16, 253-260 https://doi.org/10.1002/elps.1150160141
  21. Plass, C., Shibata, H., Kalcheva, I., Mullins, L., Kotelevtseva, N., Mullins, J., Kato, R., Sasaki, H., Hirotsune, S., Okazaki, Y., Held, W.A, Hayashizaki, Y. and Chapman, V.M (1996). Identification of Grf1 on mouse chromosome 9 as an imprinted gene by RLGS-M. Nat. Genet. 14, 106-109 https://doi.org/10.1038/ng0996-106
  22. Pohlmann, P., DiLeone, L.P., Cancella, A.I., Caldas, A.P., Dal Lago, L., Campos, O.Jr., Monego, E., Rivoire, W., and Schwartsmann, G. (2002).Phase II trial of cisplatin plus decitabine, a new DNA hypomethylating agent, in patients with advanced squamous cell carcinoma of the cervix. Am. J. Clin. Oncol. 25, 496-501 https://doi.org/10.1097/00000421-200210000-00015
  23. Shibata, H., Yoshino, K., Muramatsu, M., Plass, C., Chapman, V.M., and Hayashizaki, Y. (1995). The use of restriction landmark genomic scanning to scan the mouse genome for endogenous loci with imprinted patterns of methylation. Electrophoresis 16, 210-217 https://doi.org/10.1002/elps.1150160136
  24. Smiraglia, D.J., Fruhwald, M.C., Costello, J.F., McCormick, S.P., Dai, Z., Peltomaki, P., O'Dorisio, M.S., Cavenee, W.K., and Plass, C. (1999). A new tool for the rapid cloning of amplified and hypermethylated human DNA sequences from restriction landmark genome scanning gels. Genomics 58, 254-262 https://doi.org/10.1006/geno.1999.5840
  25. Smiraglia, D.J., Rush, L.J., Fruhwald, M.C., Dai, Z., Held, W.A, Costello, J.F., Lang, J.C., Eng, C., Li, B., Wright, F.A, Caligiuri, M.A, and Plass, C. (2001). Excessive CpG island hypermethylation in cancer cell lines versus primary human malignancies. Hum. Mol. Genet. 10, 1413-1419 https://doi.org/10.1093/hmg/10.13.1413
  26. Smiraglia, D.J., Szymanska,J., Kraggerud, S.M., Lothe,R.A, Peltomaki, P., and Plass, C. (2002). Distinct epigenetic phenotypes in seminomatous and nonseminomatous testicular germ cell tumors. Oncogene 21, 3909-3916 https://doi.org/10.1038/sj.onc.1205488
  27. Rush, L.J., Dai, Z., Smiraglia, D.J., Gao, X., Wright, F.A, Fruhwald, M., Costello, J.F., Held, W.A, Yu, L., Krahe, R., Kolitz, J.E., Bloomfield, C.D., Caligiuri, M.A, and Plass, C. (2001). Novel methylation targets in de novo acute myeloid leukemia with prevalence of chromosome 11 loci. Blood97, 3226-3233 https://doi.org/10.1182/blood.V97.10.3226
  28. Rush, L.J., Raval, A., Funchain, P., Johnson, A.J., Smith, L., Lucas, D.M., Bembea, M., Liu, T.H., Heerema, N.A., Rassenti, L., Liyanarachchi, S., Davuluri, R., Byrd, J.C., and Plass, C. (2004). Epigenetic profiling in chronic lymphocytic leukemia reveals novel methylation targets. Cancer Res. 64, 2424-2433 https://doi.org/10.1158/0008-5472.CAN-03-2870
  29. Zardo, G., Tiirikainen, M.I., Hong, C., Misra, A., Feuerstein, B.G., Volik, S., Collins, C.C., Lamborn, K.R., Bollen, A., Pinkel, D., Albertson, D.G., and Costello, J.F. (2002). Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors. Nat.Genet. 32, 453-458 https://doi.org/10.1038/ng1007