Analysis of CpG island methylation using Rolling Circle Amplification (RCA) product microarray

Journal of Biomedical Nanotechnology

Volumn 7, Issue 2, 2011, Pages 292-299

  Zhao, Hong ^a   Ma, Xiaodong ^a   Li, Minli ^a   Zhou, Dongrui ^b   Xiao, Pengfeng ^a   Lu, Zuhong ^a,b  

^a SOUTHEAST UNIVERSITY   (China)

^b Southeast University   (China)

Author keywords

Methylation; Microarray; Padlock probe; Rolling circle amplification

Indexed keywords

CPG ISLANDS; DNA MICRO-ARRAY; DNA SAMPLES; GENOMIC DNA; HIGH-THROUGHPUT DETECTION; METHYLATION ANALYSIS; METHYLATION-SPECIFIC PCR; MICROARRAY DATA; PCR PRODUCTS; ROLLING CIRCLE AMPLIFICATION; ROLLING CIRCLE AMPLIFICATIONS; TARGET GENES;

GENES; LOCKS (FASTENERS); METHYLATION; MICROARRAYS; POLYMERASE CHAIN REACTION; PROBES;

ALKYLATION;

BISULFITE; GENOMIC DNA; PROTEIN P16; SINGLE STRANDED DNA; SOMATOMEDIN BINDING PROTEIN; SOMATOMEDIN BINDING PROTEIN 7; UNCLASSIFIED DRUG; DNA; INSULIN LIKE GROWTH FACTOR BINDING PROTEIN RELATED PROTEIN 1; INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN-RELATED PROTEIN 1;

ALLELE; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; DNA PROBE; GENE TARGETING; HUMAN; HUMAN CELL; HUMAN TISSUE; HYBRIDIZATION; IMMOBILIZATION; MICROTECHNOLOGY; NUCLEIC ACID AMPLIFICATION; POLYMERASE CHAIN REACTION; ROLLING CIRCLE AMPLIFICATION PRODUCT MICROARRAY; BLOOD; BREAST TUMOR; CHEMISTRY; FEMALE; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; STATISTICAL MODEL; TUMOR CELL LINE; TUMOR SUPPRESSOR GENE;

BASE SEQUENCE; BREAST NEOPLASMS; CELL LINE, TUMOR; CPG ISLANDS; DNA; DNA METHYLATION; DNA, NEOPLASM; FEMALE; GENES, P16; HUMANS; INSULIN-LIKE GROWTH FACTOR BINDING PROTEINS; LINEAR MODELS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID AMPLIFICATION TECHNIQUES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 79961012866     PISSN: 15507033     EISSN: 15507041     Source Type: Journal    
DOI: 10.1166/jbn.2011.1287     Document Type: Article

References (43)

1. X. Nan, H. H. Ng, C. A. Johnson, C. D. Laherty, B. M. Turner, R. N. Eisenman, and A. Bird, Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393, 386 (1998).
2. P. L. Jones, G. J. Veenstra, P. A. Wade, D. Vermaak, S. U. Kass, N. Landsberger, J. Strouboulis, and A. P. Wolffe, Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat. Genet. 19, 187 (1998).
3. A. G. Knudson, Chasing the cancer demon. Annu. Rev. Genet. 34, 1 (2000).
4. P. A. Jones and S. B. Baylin, The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 3, 415 (2002).
5. M. R. Rountree, K. E. Bachman, J. G. Herman, and S. B. Baylin, DNA methylation, chromatin inheritance, and cancer. Oncogene 20, 3156 (2001).
6. P. A. Jones, Epigenetics in carcinogenesis and cancer prevention. Ann. N. Y. Acad. Sci. 983, 213 (2003).
7. M. Widschwendter and P. A. Jones, The potential prognostic, predictive, and therapeutic values of DNA methylation in cancer. Clin. Cancer. Res. 8, 17 (2002).
8. S. E. Cottrell, Molecular diagnostic applications of DNA methylation technology. Clin. Biochem. 37, 595 (2004).
9. P. S. Yan, C. M. Chen, H. Shi, F. Rahmatpanah, S. H. Wei, C. W. Caldwell, and T. H. Huang, Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays. Cancer. Res. 61, 8375 (2001).
10. J. G. Herman, J. R. Graff, S. Myohanen, B. Nelkin, and S. B. Baylin, Methylation-specific PCR: A novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA 93, 9821 (1996).
11. C. Goessl, M. Müller, and K. Miller, Methylation-specific PCR (MSP) for detection of tumour DNA in the blood plasma and serum of patients with prostate cancer. Prostate. Cancer. Prostatic. Dis. 3, S17 (2000).
12. T. Swift-Scanlan, A. Blackford, P. Argani, S. Sukumar, and M. J. Fackler, Two-color quantitative multiplex methylation-specific PCR. Biotechniques 40, 210 (2006).
13. R. J. Esther, R. Bhattacharya, M. Ruan, M. E. Bolander, D. Mukhopadhyay, G. Sarkar, and P. Mukherjee, Gold nanoparticles do not affect the global transcriptional program of human umbilical vein endothelial cells: A DNA-microarray analysis. J. Biomed. Nanotechnol. 1, 328 (2005).
14. B. Cherif, C. L. Villiers, G. Paranhos-Baccala, R. Calemczuk, P. N. Marche, T. Livache, and M. B. Villiers, Design and application of a microarray for fluorescence and surface plasmon resonance imaging analysis of peptide-antibody interactions. J. Biomed. Nanotechnol. 2, 29 (2006).
15. L. Cheng, Q. Y. Ge, B. L. Sun, P. F. Yu, X. Y. Ke, and Z. H. Lu, Polyacrylamide gel-based microarray: A novel method applied to the association study between the polymorphisms of BDNF gene and autism. J. Biomed. Nanotechnol. 5, 542 (2009).
16. L. Tian, S. Li, H. N. Liu, Z. F. Wang, and N. Y. He, An automated magstation for high-throughput single nucleotide polymorphism genotyping and the dual-color hybridization. J. Biomed. Nanotechnol. 5, 511 (2009).
17. H. N. Liu, S. Li, L. S. Liu, L. Tian, and N. Y. He, An integrated and sensitive detection platform for biosensing application based on Fe@Au magnetic nanoparticles as bead array carries. Biosens. Bioelectron. 26, 1442 (2010).
18. S. Li, H. N. Liu, and N. Y. He, Covalent binding of streptavidin on gold magnetic nanoparticles for bead array fabrication. J. Nanosci. Nanotechnol. 10, 4875 (2010).
19. S. Li, H. N. Liu, L. S. Liu, L. Tian, and N. Y. He, A novel automated assay with dual-color hybridization for single-nucleotide 4 polymorphisms genotyping on gold magnetic nanoparticle array. Anal. Biochem. 405, 141 (2010).
20. R. S. Gitan, H. Shi, C. M. Chen, P. S. Yan, and T. H. Huang, Methylation specific oligonucleotide microarray: A new potential for high throughput methylation analysis. Genome. Res. 12, 158 (2002).
21. P. Hou, M. J. Ji, S. Li, N. Y. He, and Z. H. Lu, High-throughput method for detecting DNA methylation. J. Biochem. Biophys. Methods. 60, 139 (2004).
22. D. R. Zhou, W. Q. Qiao, Y. Wan, and Z. H. Lu, Microarray-based methylation analysis using dual-color fluorescence hybridization. J. Biochem. Biophys. Methods 66, 33 (2006).
23. R. Shen, J. B. Fan, D. Campbell, W. Chang, J. Chen, D. Doucet, J. Yeakley, M. Bibikova, G. E. Wickham, C. McBride, F. Steemers, F. Garcia, B. G. Kermani, K. Gunderson, and A. Oliphant, High-throughput SNP genotyping on universal bead arrays. Mutat Res. 573, 70 (2005).
24. E. Ozkumur, S. Ahn, A. Yalcin, C. A. Lopez, E. Cevik, R. J. Irani, C. DeLisi, M. Chiari, and M. S. Unlu, Label-free microarray imaging for direct detection of DNA hybridization and single-nucleotide mismatches. Biosens. Bioelectron. 25, 1789 (2010).
25. X. R. Duan, L. B. Liu, and S. Wang, Homogeneous and one-step fluorescent allele-specific PCR for SNP genotyping assays using conjugated polyelectrolytes. Biosens. Bioelectron. 24, 2095 (2009).
26. T. Matsunaga, K. Maruyama, H. Takeyama, and T. Katoh, High-throughput SNP detection using nano-scale engineered biomagnetite. Biosens. Bioelectron. 22, 2315 (2007).
27. Y. Z. Zheng, X. Y. Ke, Y. Zhou, M. H. Zhang, P. Chen, and Z. H. Lu, Detection of multiple SNPs in numerous samples with polyacrylamide gel-based microarray. J. Nanosci. Nanotechnol. 10, 479 (2010).
28. H. N. Liu, S. Li, L. Tian, L. S. Liu, and N. Y. He, A novel single nucleotide polymorphisms detection sensors based on magnetic nanoparticles array and dual-color single base extension. J. Nanosci. Nanotechnol. 10, 5311 (2010).
29. H. N. Liu, S. Li, M. J. Ji, L. B. Nie, J. R. Chen, Y. Q. Miao, and N. Y. He, Fabrication and application of single nucleotide polymorphisms library on magnetic nanoparticles using adaptor PCR. J. Nanosci. Nanotechnol. 8, 405 (2008).
30. Z. P. Li and H. Kambara, Single nucleotide polymorphism analysis based on minisequencing coupled with a fluorescence microsphere technology. J. Nanosci. Nanotechnol. 5, 1256 (2005).
31. M. Nilsson, K. Krejci, J. Koch, M. Kwiatkowski, P. Gustavsson, and U. Landegren, Padlock probes reveal single-nucleotide differences, parent of origin and in situ distribution of centromeric sequences in human chromosomes 13 and 21. Nat. Genet. 16, 252 (1997).
32. M. Nilsson, H. Malmgren, M. Samiotaki, M. Kwiatkowski, B. P. Chowdhary, and U. Landegren, Padlock probes: Circularizing oligonucleotides for localized DNA detection. Science 265, 2085 (1994).
33. J. Baner, M. Nilsson, M. Mendel-Hartvig, and U. Landegren, Signal amplification of padlock probes by rolling circle replication. Nucleic. Acids. Res. 26, 5073 (1998).
34. X. Qi, S. Bakht, K. M. Devos, M. D. Gale, and A. Osbourn, L-RCA (ligation-rolling circle amplification): A general method for genotyping of single nucleotide polymorphisms (SNPs). Nucleic. Acids. Res. 29, E116 (2001).
35. P. M. Lizardi, X. Huang, Z. Zhu, P. Bray-Ward, D. C. Thomas, and D. C. Ward, Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat. Genet. 19, 225 (1998).
36. X. J. Li, J. F. Luo, P. F. Xiao, X. L. Shi, C. Tang, and Z. H. Lu, Genotyping of multiple single nucleotide polymorphisms with hyperbranched rolling circle amplification and microarray. Clin. Chim. Acta. 399, 40 (2009).
37. S. Komatsu, Y. Okazaki, M. Tateno, J. Kawai, H. konno, M. Kusakabe, A. Yoshiki, M. Muramatsu, W. A. Held, and Y. Hayashizaki, Methylation and down regulated expression of mac25/insulin-like growth factor binding protein-7 is associated with liver tumorigenesis in SV40T/t antigen transgenic mice, screened by Restriction Landmark Genomic Scanning for Methylation (RLGSM). Biochem. Biophys. Res. Commun. 267, 109 (2000).
38. N. H. Nielsen, G. Roos, S. O. Emdin, and G. Landberg, Methylation of the p16 (Ink4a) tumor suppressor gene 5′-CpG island in breast cancer. Cancer. Lett. 163, 59 (2001).
39. M. Frommer, L. E. McDonald, D. S. Millar, C. M. Collis, F. Watt, G. W. Grigg, P. L. Molloy, and C. L. Paul, A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. USA 89, 1827 (1992).
40. S. J. Clark, J. Harrison, C. L. Paul, and M. Frommer, High sensitivity mapping of methylated cytosines. Nucleic. Acids. Res. 22, 2990 (1994).
41. P. F. Xiao, L. Cheng, Y. Wan, B. L. Sun, Z. Z. Chen, S. Y. Zhang, C. Z. Zhang, G. H. Zhou, and Z. H. Lu, An improved gel-based DNA microarray method for detecting single nucleotide mismatch. Electrophoresis 27, 3904 (2006).
42. A. F. Faruqi, S. Hosono, M. D. Driscoll, F. B. Dean, O. Alsmadi, R. Bandaru, G. Kumar, B. Grimwade, Q. Zong, Z. Sun, Y. Du, S. Kingsmore, T. Knott, and R. S. Lasken, High-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification. BMC Genomics 2, 4 (2001).
43. A. Y. Rubina, S. V. Pan'kov, E. I. Dementieva, D. N. Pen'kov, A. V. Butygin, V. A. Vasiliskov, A. V. Chudinov, A. L. Mikheikin, V. M. Mikhailovich, and A. D. Mirzabekov, Hydrogel drop microchips with immobilized DNA: Properties and methods for large-scale production. Anal. Biochem. 325, 92 (2004).